Implement loading lua from separate files via @

To be less retarded...

.gitignore

@@ -1,2 +1,4 @@
 *.exe
 .qodo
+*.sqlite
+.cursor/rules

.vscode/launch.json

@@ -12,11 +12,23 @@
 			"program": "${workspaceFolder}",
 			"cwd": "C:/Users/Administrator/Seafile/Games-Barotrauma",
 			"args": [
-				"loglevel",
+				"-loglevel",
 				"trace",
-				"(?-s)LightComponent!anyrange=\"(!num)\"",
-				"*4",
-				"**/Outpost*.xml"
+				"-cook",
+				"*.yml",
+			]
+		},
+		{
+			"name": "Launch Package (Payday 2)",
+			"type": "go",
+			"request": "launch",
+			"mode": "auto",
+			"program": "${workspaceFolder}",
+			"cwd": "C:/Users/Administrator/Seafile/Games-Payday2",
+			"args": [
+				"-loglevel",
+				"trace",
+				"*.yml",
 			]
 		},
 		{
@@ -33,18 +45,71 @@
 				"cookassistant.yml",
 			]
 		},
+		{
+			"name": "Launch Package (Quasimorph cookfile)",
+			"type": "go",
+			"request": "launch",
+			"mode": "auto",
+			"program": "${workspaceFolder}",
+			"cwd": "C:/Users/Administrator/Seafile/Games-Quasimorph",
+			"args": [
+				"cook.yml",
+			]
+		},
+		{
+			"name": "Launch Package (Rimworld cookfile)",
+			"type": "go",
+			"request": "launch",
+			"mode": "auto",
+			"program": "${workspaceFolder}",
+			"cwd": "C:/Users/Administrator/Seafile/Games-Rimworld/294100",
+			"args": [
+				"cookVehicles.yml",
+			]
+		},
 		{
 			"name": "Launch Package (Workspace)",
 			"type": "go",
 			"request": "launch",
 			"mode": "auto",
 			"program": "${workspaceFolder}",
+			"args": [
+				"tester.yml",
+			]
+		},
+		{
+			"name": "Launch Package (Avorion)",
+			"type": "go",
+			"request": "launch",
+			"mode": "auto",
+			"program": "${workspaceFolder}",
+			"cwd": "C:/Users/Administrator/Seafile/Games-Avorion/Avorion",
+			"args": [
+				"*.yml",
+			]
+		},
+		{
+			"name": "Launch Package (Minecraft)",
+			"type": "go",
+			"request": "launch",
+			"mode": "auto",
+			"program": "${workspaceFolder}",
+			"cwd": "C:/Users/Administrator/Seafile/Games-Minecraft",
+			"args": [
+				"cook_tacz.yml",
+			]
+		},
+		{
+			"name": "Launch Package (ICARUS)",
+			"type": "go",
+			"request": "launch",
+			"mode": "auto",
+			"program": "${workspaceFolder}",
+			"cwd": "C:/Users/Administrator/Seafile/Games-ICARUS/Icarus/Saved/IME3/Mods",
 			"args": [
 				"-loglevel",
 				"trace",
-				"(?-s)LightComponent!anyrange=\"(!num)\"",
-				"*4",
-				"**/Outpost*.xml"
+				"cook_processorrecipes.yml",
 			]
 		}
 	]

README.md

@@ -16,6 +16,7 @@ A Go-based tool for modifying XML, JSON, and text documents using XPath/JSONPath
   - String manipulations
   - Date conversions
   - Structural changes
+  - CSV/TSV parsing with comments and headers
   - Whole ass Lua environment
 - **Error Handling**: Comprehensive error detection for:
   - Invalid XML/JSON
@@ -101,6 +102,87 @@ chef -xml "//item" "if tonumber(v.stock) > 0 then v.price = v.price * 0.8 end" i
 <item stock="5" price="8.00"/>
 ```
 
+### 6. CSV/TSV Processing
+The Lua environment includes CSV parsing functions that support comments, headers, and custom delimiters.
+
+```lua
+-- Basic CSV parsing
+local rows = fromCSV(csvText)
+
+-- With options
+local rows = fromCSV(csvText, {
+    delimiter = "\t",        -- Tab delimiter for TSV (default: ",")
+    hasHeaders = true,       -- First row is headers (default: false)
+    hasComments = true       -- Filter lines starting with # (default: false)
+})
+
+-- Access by index
+local value = rows[1][2]
+
+-- Access by header name (when hasHeaders = true)
+local value = rows[1].Name
+
+-- Convert back to CSV
+local csv = toCSV(rows, "\t")  -- Optional delimiter parameter
+```
+
+**Example with commented TSV file:**
+```lua
+-- Input file:
+-- #mercenary_profiles
+-- Id	Name	Value
+-- 1	Test	100
+-- 2	Test2	200
+
+local csv = readFile("mercenaries.tsv")
+local rows = fromCSV(csv, {
+    delimiter = "\t",
+    hasHeaders = true,
+    hasComments = true
+})
+
+-- Access data
+rows[1].Name  -- "Test"
+rows[2].Value -- "200"
+```
+
+## Lua Helper Functions
+
+The Lua environment includes many helper functions:
+
+### Math Functions
+- `min(a, b)`, `max(a, b)` - Min/max of two numbers
+- `round(x, n)` - Round to n decimal places
+- `floor(x)`, `ceil(x)` - Floor/ceiling functions
+
+### String Functions
+- `upper(s)`, `lower(s)` - Case conversion
+- `trim(s)` - Remove leading/trailing whitespace
+- `format(s, ...)` - String formatting
+- `strsplit(inputstr, sep)` - Split string by separator
+
+### CSV Functions
+- `fromCSV(csv, options)` - Parse CSV/TSV text into table of rows
+  - Options: `delimiter` (default: ","), `hasHeaders` (default: false), `hasComments` (default: false)
+- `toCSV(rows, delimiter)` - Convert table of rows back to CSV text
+
+### Conversion Functions
+- `num(str)` - Convert string to number (returns 0 if invalid)
+- `str(num)` - Convert number to string
+- `is_number(str)` - Check if string is numeric
+
+### Table Functions
+- `isArray(t)` - Check if table is a sequential array
+- `dump(table, depth)` - Print table structure recursively
+
+### HTTP Functions
+- `fetch(url, options)` - Make HTTP request, returns response table
+  - Options: `method`, `headers`, `body`
+  - Returns: `{status, statusText, ok, body, headers}`
+
+### Regex Functions
+- `re(pattern, input)` - Apply regex pattern, returns table with matches
+
 ## Installation
 
 ```bash

cmd/log_format_test/main.go

@@ -1,27 +0,0 @@
-package main
-
-import (
-	"modify/logger"
-	"time"
-)
-
-func main() {
-	// Initialize logger with DEBUG level
-	logger.Init(logger.LevelDebug)
-
-	// Test different log levels
-	logger.Info("This is an info message")
-	logger.Debug("This is a debug message")
-	logger.Warning("This is a warning message")
-	logger.Error("This is an error message")
-	logger.Trace("This is a trace message (not visible at DEBUG level)")
-
-	// Test with a goroutine
-	logger.SafeGo(func() {
-		time.Sleep(10 * time.Millisecond)
-		logger.Info("Message from goroutine")
-	})
-
-	// Wait for goroutine to complete
-	time.Sleep(20 * time.Millisecond)
-}

example_cook.toml

@@ -0,0 +1,544 @@
+# Global variables - available to all commands
+[variables]
+foobar = 4
+multiply = 1.5
+prefix = 'NEW_'
+enabled = true
+
+# Multi-regex example using variable in Lua
+[[commands]]
+name = 'RFToolsMultiply'
+regexes = [
+    'generatePerTick = !num',
+    'ticksPer\w+ = !num',
+    'generatorRFPerTick = !num',
+]
+lua = '* foobar'
+files = [
+    'polymc/instances/**/rftools*.toml',
+    'polymc\instances\**\rftools*.toml',
+]
+reset = true
+
+# Named capture groups with arithmetic and string ops
+[[commands]]
+name = 'UpdateAmountsAndItems'
+regex = '(?P<amount>!num)\s+units\s+of\s+(?P<item>[A-Za-z_\-]+)'
+lua = 'amount = amount * multiply; item = upper(item); return true'
+files = ['data/**/*.txt']
+
+# Full replacement via Lua 'replacement' variable
+[[commands]]
+name = 'BumpMinorVersion'
+regex = 'version\s*=\s*"(?P<major>!num)\.(?P<minor>!num)\.(?P<patch>!num)"'
+lua = 'replacement = format("version=\"%s.%s.%s\"", major, num(minor)+1, 0); return true'
+files = ['config/*.ini', 'config/*.cfg']
+
+# TOML multiline regex example - single quotes make regex natural!
+[[commands]]
+name = 'StressValues'
+regex = '''
+\[kinetics\.stressValues\.v2\.capacity\]
+    steam_engine = !num
+    water_wheel = !num
+    copper_valve_handle = !num
+    hand_crank = !num
+    creative_motor = !num'''
+lua = 'v1 * multiply'
+files = ['*.txt']
+isolate = true
+
+# Network configuration with complex multiline regex
+[[commands]]
+name = 'NetworkConfig'
+regex = '''
+networking\.firewall\.allowPing = true
+networking\.firewall\.allowedTCPPorts = \[ 47984 47989 47990 \]
+networking\.firewall\.allowedUDPPortRanges = \[
+    \{ from = \d+; to = \d+; \}
+    \{ from = 8000; to = 8010; \}
+\]'''
+lua = "replacement = string.gsub(block[1], 'true', 'false')"
+files = ['*.conf']
+isolate = true
+
+# Simple regex with single quotes - no escaping needed!
+[[commands]]
+name = 'EnableFlags'
+regex = 'enabled\s*=\s*(true|false)'
+lua = '= enabled'
+files = ['**/*.toml']
+
+# Demonstrate NoDedup to allow overlapping replacements
+[[commands]]
+name = 'OverlappingGroups'
+regex = '(?P<a>!num)(?P<b>!num)'
+lua = 'a = num(a) + 1; b = num(b) + 1; return true'
+files = ['overlap/**/*.txt']
+nodedup = true
+
+# Isolate command example operating on entire matched block
+[[commands]]
+name = 'IsolateUppercaseBlock'
+regex = '''BEGIN
+(?P<block>!any)
+END'''
+lua = 'block = upper(block); return true'
+files = ['logs/**/*.log']
+loglevel = 'TRACE'
+isolate = true
+
+# Using !rep placeholder and arrays of files
+[[commands]]
+name = 'RepeatPlaceholderExample'
+regex = 'name: (.*) !rep(, .* , 2)'
+lua = '-- no-op, just demonstrate placeholder; return false'
+files = ['lists/**/*.yml', 'lists/**/*.yaml']
+
+# Using string variable in Lua expression
+[[commands]]
+name = 'PrefixKeys'
+regex = '(?P<key>[A-Za-z0-9_]+)\s*='
+lua = 'key = prefix .. key; return true'
+files = ['**/*.properties']
+
+# HTTP fetch example - get version from API and update config
+[[commands]]
+name = 'UpdateVersionFromAPI'
+regex = 'version\s*=\s*"(?P<version>[^"]+)"'
+lua = '''
+local response = fetch("https://api.example.com/version", {
+    method = "GET",
+    headers = { ["Accept"] = "application/json" }
+})
+if response and response.body then
+    local data = fromJSON(response.body)
+    if data.latest then
+        version = data.latest
+        return true
+    end
+end
+return false
+'''
+files = ['version.conf']
+
+# Complex multiline block replacement with state machine
+[[commands]]
+name = 'ModifyConfigBlock'
+regex = '''(?x)
+\[server\]
+\s+host\s*=\s*"(?P<host>[^"]+)"
+\s+port\s*=\s*(?P<port>\d+)
+\s+ssl\s*=\s*(?P<ssl>true|false)'''
+lua = '''
+port = num(port) + 1000
+ssl = "true"
+replacement = format('[server]\n  host = "%s"\n  port = %d\n  ssl = %s', host, port, ssl)
+return true
+'''
+files = ['server.conf']
+
+# Regex with !any to capture entire sections
+[[commands]]
+name = 'WrapInComment'
+regex = 'FEATURE_START\n(?P<feature>!any)\nFEATURE_END'
+lua = '''
+replacement = "FEATURE_START\n# " .. feature:gsub("\n", "\n# ") .. "\nFEATURE_END"
+return true
+'''
+files = ['features/**/*.txt']
+
+# Advanced capture groups with complex logic
+[[commands]]
+name = 'UpdateDependencies'
+regex = 'dependency\("(?P<group>[^"]+)", "(?P<name>[^"]+)", "(?P<version>[^"]+)"\)'
+lua = '''
+local major, minor, patch = version:match("(%d+)%.(%d+)%.(%d+)")
+if major and minor and patch then
+    -- Bump minor version
+    minor = num(minor) + 1
+    version = format("%s.%s.0", major, minor)
+    return true
+end
+return false
+'''
+files = ['build.gradle', 'build.gradle.kts']
+
+# JSON mode examples - modify single field
+[[commands]]
+name = 'JSONModifyField'
+json = true
+lua = '''
+data.value = 84
+modified = true
+'''
+files = ['data/**/*.json']
+
+# JSON mode - add new field
+[[commands]]
+name = 'JSONAddField'
+json = true
+lua = '''
+data.newField = "added"
+modified = true
+'''
+files = ['config/**/*.json']
+
+# JSON mode - modify nested fields
+[[commands]]
+name = 'JSONNestedModify'
+json = true
+lua = '''
+if data.config and data.config.settings then
+    data.config.settings.enabled = true
+    data.config.settings.timeout = 60
+    modified = true
+end
+'''
+files = ['settings/**/*.json']
+
+# JSON mode - modify array elements
+[[commands]]
+name = 'JSONArrayMultiply'
+json = true
+lua = '''
+if data.items then
+    for i, item in ipairs(data.items) do
+        data.items[i].value = item.value * multiply
+    end
+    modified = true
+end
+'''
+files = ['data/**/*.json']
+
+# JSON mode - modify object version
+[[commands]]
+name = 'JSONObjectUpdate'
+json = true
+lua = '''
+data.version = "2.0.0"
+data.enabled = enabled
+modified = true
+'''
+files = ['config/**/*.json']
+
+# JSON mode - surgical editing of specific row
+[[commands]]
+name = 'JSONSurgicalEdit'
+json = true
+lua = '''
+if data.Rows and data.Rows[1] then
+    data.Rows[1].Weight = 999
+    modified = true
+end
+'''
+files = ['items/**/*.json']
+
+# JSON mode - remove array elements conditionally
+[[commands]]
+name = 'JSONRemoveDisabled'
+json = true
+lua = '''
+if data.features then
+    local i = 1
+    while i <= #data.features do
+        if data.features[i].enabled == false then
+            table.remove(data.features, i)
+        else
+            i = i + 1
+        end
+    end
+    modified = true
+end
+'''
+files = ['config/**/*.json']
+
+# JSON mode - deep nested object manipulation
+[[commands]]
+name = 'JSONDeepUpdate'
+json = true
+lua = '''
+if data.game and data.game.balance and data.game.balance.economy then
+    local econ = data.game.balance.economy
+    econ.inflation = (econ.inflation or 1.0) * 1.05
+    econ.taxRate = 0.15
+    econ.lastUpdate = os.date("%Y-%m-%d")
+    modified = true
+end
+'''
+files = ['settings/**/*.json']
+
+# JSON mode - iterate and transform all matching objects
+[[commands]]
+name = 'JSONTransformItems'
+json = true
+lua = '''
+local function processItem(item)
+    if item.type == "weapon" and item.damage then
+        item.damage = item.damage * multiply
+        item.modified = true
+    end
+end
+
+if data.items then
+    for _, item in ipairs(data.items) do
+        processItem(item)
+    end
+    modified = true
+elseif data.inventory then
+    for _, item in ipairs(data.inventory) do
+        processItem(item)
+    end
+    modified = true
+end
+'''
+files = ['data/**/*.json']
+
+# CSV processing example - read, modify, write
+[[commands]]
+name = 'CSVProcess'
+regex = '(?P<csv>!any)'
+lua = '''
+local rows = fromCSV(csv, { hasheader = true })
+for i, row in ipairs(rows) do
+    if row.Value then
+        row.Value = num(row.Value) * multiply
+    end
+end
+replacement = toCSV(rows, { hasheader = true })
+return true
+'''
+files = ['data/**/*.csv']
+
+# CSV processing with custom delimiter (TSV)
+[[commands]]
+name = 'TSVProcess'
+regex = '(?P<tsv>!any)'
+lua = '''
+local rows = fromCSV(tsv, { delimiter = "\t", hasheader = true, hascomments = true })
+for i, row in ipairs(rows) do
+    if row.Price then
+        row.Price = num(row.Price) * 1.1
+    end
+end
+replacement = toCSV(rows, { delimiter = "\t", hasheader = true })
+return true
+'''
+files = ['data/**/*.tsv']
+
+# CSV processing - modify specific columns
+[[commands]]
+name = 'CSVModifyColumns'
+regex = '(?P<csv>!any)'
+lua = '''
+local rows = fromCSV(csv, { hasheader = true })
+for i, row in ipairs(rows) do
+    if row.Name then
+        row.Name = prefix .. row.Name
+    end
+    if row.Status then
+        row.Status = upper(row.Status)
+    end
+end
+replacement = toCSV(rows, { hasheader = true })
+return true
+'''
+files = ['exports/**/*.csv']
+
+# XML mode - multiply numeric attributes using helper functions
+[[commands]]
+name = 'XMLMultiplyAttributes'
+regex = '(?P<xml>!any)'
+lua = '''
+visitElements(data, function(elem)
+    if elem._tag == "Item" then
+        modifyNumAttr(elem, "Weight", function(val) return val * multiply end)
+        modifyNumAttr(elem, "Value", function(val) return val * foobar end)
+    end
+end)
+modified = true
+'''
+files = ['game/**/*.xml']
+
+# XML mode - modify specific element attributes
+[[commands]]
+name = 'XMLUpdateAfflictions'
+regex = '(?P<xml>!any)'
+lua = '''
+local afflictions = findElements(data, "Affliction")
+for _, affliction in ipairs(afflictions) do
+    local id = getAttr(affliction, "identifier")
+    if id == "burn" or id == "bleeding" then
+        modifyNumAttr(affliction, "strength", function(val) return val * 0.5 end)
+        setAttr(affliction, "description", "Weakened effect")
+    end
+end
+modified = true
+'''
+files = ['config/Afflictions.xml']
+
+# XML mode - add new elements using helpers
+[[commands]]
+name = 'XMLAddItems'
+regex = '(?P<xml>!any)'
+lua = '''
+local items = findFirstElement(data, "Items")
+if items then
+    local newItem = {
+        _tag = "Item",
+        _attr = {
+            identifier = "new_item",
+            Weight = "10",
+            Value = "500"
+        }
+    }
+    addChild(items, newItem)
+    modified = true
+end
+'''
+files = ['items/**/*.xml']
+
+# XML mode - remove elements by attribute value
+[[commands]]
+name = 'XMLRemoveDisabled'
+regex = '(?P<xml>!any)'
+lua = '''
+visitElements(data, function(elem)
+    if elem._tag == "Feature" and getAttr(elem, "enabled") == "false" then
+        -- Mark for removal (actual removal happens via parent)
+        elem._remove = true
+    end
+end)
+
+-- Remove marked children
+visitElements(data, function(elem)
+    if elem._children then
+        local i = 1
+        while i <= #elem._children do
+            if elem._children[i]._remove then
+                table.remove(elem._children, i)
+            else
+                i = i + 1
+            end
+        end
+    end
+end)
+
+modified = true
+'''
+files = ['config/**/*.xml']
+
+# XML mode - conditional attribute updates based on other attributes
+[[commands]]
+name = 'XMLConditionalUpdate'
+regex = '(?P<xml>!any)'
+lua = '''
+visitElements(data, function(elem)
+    if elem._tag == "Weapon" then
+        local tier = getAttr(elem, "tier")
+        if tier and num(tier) >= 3 then
+            -- High tier weapons get damage boost
+            modifyNumAttr(elem, "damage", function(val) return val * 1.5 end)
+            setAttr(elem, "rarity", "legendary")
+        end
+    end
+end)
+modified = true
+'''
+files = ['weapons/**/*.xml']
+
+# XML mode - modify nested elements
+[[commands]]
+name = 'XMLNestedModify'
+regex = '(?P<xml>!any)'
+lua = '''
+local config = findFirstElement(data, "Configuration")
+if config then
+    local settings = findFirstElement(config, "Settings")
+    if settings then
+        setAttr(settings, "timeout", "120")
+        setAttr(settings, "maxRetries", "5")
+        
+        -- Add or update nested element
+        local logging = findFirstElement(settings, "Logging")
+        if not logging then
+            logging = {
+                _tag = "Logging",
+                _attr = { level = "DEBUG", enabled = "true" }
+            }
+            addChild(settings, logging)
+        else
+            setAttr(logging, "level", "INFO")
+        end
+    end
+end
+modified = true
+'''
+files = ['config/**/*.xml']
+
+# XML mode - batch attribute operations
+[[commands]]
+name = 'XMLBatchAttributeUpdate'
+regex = '(?P<xml>!any)'
+lua = '''
+-- Update all Price attributes across entire document
+visitElements(data, function(elem)
+    if hasAttr(elem, "Price") then
+        modifyNumAttr(elem, "Price", function(val) return val * 1.1 end)
+    end
+    if hasAttr(elem, "Cost") then
+        modifyNumAttr(elem, "Cost", function(val) return val * 0.9 end)
+    end
+end)
+modified = true
+'''
+files = ['economy/**/*.xml']
+
+# XML mode - clone and modify elements
+[[commands]]
+name = 'XMLCloneItems'
+regex = '(?P<xml>!any)'
+lua = '''
+local items = findElements(data, "Item")
+local newItems = {}
+
+for _, item in ipairs(items) do
+    local id = getAttr(item, "identifier")
+    if id and id:match("^weapon_") then
+        -- Clone weapon as upgraded version
+        local upgraded = {
+            _tag = "Item",
+            _attr = {
+                identifier = id .. "_mk2",
+                Weight = getAttr(item, "Weight"),
+                Value = tostring(num(getAttr(item, "Value")) * 2)
+            }
+        }
+        table.insert(newItems, upgraded)
+    end
+end
+
+-- Add all new items
+for _, newItem in ipairs(newItems) do
+    addChild(data, newItem)
+end
+
+if #newItems > 0 then
+    modified = true
+end
+'''
+files = ['items/**/*.xml']
+
+# XML mode - remove all children with specific tag
+[[commands]]
+name = 'XMLRemoveObsolete'
+regex = '(?P<xml>!any)'
+lua = '''
+visitElements(data, function(elem)
+    -- Remove all "Deprecated" children
+    removeChildren(elem, "Deprecated")
+    removeChildren(elem, "Legacy")
+end)
+modified = true
+'''
+files = ['config/**/*.xml']

glob_test.go

@@ -1,7 +1,7 @@
 package main
 
 import (
-	"modify/utils"
+	"cook/utils"
 	"os"
 	"path/filepath"
 	"testing"
@@ -82,7 +82,7 @@ func TestGlobExpansion(t *testing.T) {
 			for _, pattern := range tc.patterns {
 				patternMap[pattern] = struct{}{}
 			}
-			files, err := utils.ExpandGLobs(patternMap)
+			files, err := utils.ExpandGlobs(patternMap)
 			if err != nil {
 				t.Fatalf("ExpandGLobs failed: %v", err)
 			}

go.mod

@@ -1,38 +1,41 @@
-module modify
+module cook
 
-go 1.24.1
+go 1.23.2
 
 require (
+	git.site.quack-lab.dev/dave/cylogger v1.3.0
 	github.com/bmatcuk/doublestar/v4 v4.8.1
 	github.com/stretchr/testify v1.10.0
 	github.com/yuin/gopher-lua v1.1.1
 	gopkg.in/yaml.v3 v3.0.1
+	gorm.io/gorm v1.30.0
 )
 
 require (
-	dario.cat/mergo v1.0.0 // indirect
-	github.com/Microsoft/go-winio v0.6.2 // indirect
-	github.com/ProtonMail/go-crypto v1.1.5 // indirect
-	github.com/cloudflare/circl v1.6.0 // indirect
-	github.com/cyphar/filepath-securejoin v0.4.1 // indirect
 	github.com/davecgh/go-spew v1.1.1 // indirect
-	github.com/emirpasic/gods v1.18.1 // indirect
-	github.com/go-git/gcfg v1.5.1-0.20230307220236-3a3c6141e376 // indirect
-	github.com/go-git/go-billy/v5 v5.6.2 // indirect
-	github.com/jbenet/go-context v0.0.0-20150711004518-d14ea06fba99 // indirect
-	github.com/kevinburke/ssh_config v1.2.0 // indirect
-	github.com/pjbgf/sha1cd v0.3.2 // indirect
+	github.com/hexops/valast v1.5.0 // indirect
+	github.com/inconshreveable/mousetrap v1.1.0 // indirect
+	github.com/jinzhu/inflection v1.0.0 // indirect
+	github.com/jinzhu/now v1.1.5 // indirect
+	github.com/kr/pretty v0.3.1 // indirect
+	github.com/mattn/go-sqlite3 v1.14.22 // indirect
 	github.com/pmezard/go-difflib v1.0.0 // indirect
-	github.com/sergi/go-diff v1.3.2-0.20230802210424-5b0b94c5c0d3 // indirect
-	github.com/skeema/knownhosts v1.3.1 // indirect
-	github.com/xanzy/ssh-agent v0.3.3 // indirect
-	golang.org/x/crypto v0.35.0 // indirect
-	golang.org/x/sys v0.30.0 // indirect
-	gopkg.in/warnings.v0 v0.1.2 // indirect
+	github.com/rogpeppe/go-internal v1.14.1 // indirect
+	github.com/spf13/pflag v1.0.9 // indirect
+	github.com/tidwall/match v1.1.1 // indirect
+	github.com/tidwall/pretty v1.2.0 // indirect
+	golang.org/x/mod v0.21.0 // indirect
+	golang.org/x/sync v0.11.0 // indirect
+	golang.org/x/text v0.22.0 // indirect
+	golang.org/x/tools v0.26.0 // indirect
+	gopkg.in/check.v1 v1.0.0-20201130134442-10cb98267c6c // indirect
+	mvdan.cc/gofumpt v0.4.0 // indirect
 )
 
 require (
-	github.com/go-git/go-git/v5 v5.14.0
-	github.com/golang/groupcache v0.0.0-20241129210726-2c02b8208cf8 // indirect
-	golang.org/x/net v0.35.0 // indirect
+	github.com/BurntSushi/toml v1.5.0
+	github.com/google/go-cmp v0.6.0
+	github.com/spf13/cobra v1.10.1
+	github.com/tidwall/gjson v1.18.0
+	gorm.io/driver/sqlite v1.6.0
 )

go.sum

@@ -1,106 +1,75 @@
-dario.cat/mergo v1.0.0 h1:AGCNq9Evsj31mOgNPcLyXc+4PNABt905YmuqPYYpBWk=
-dario.cat/mergo v1.0.0/go.mod h1:uNxQE+84aUszobStD9th8a29P2fMDhsBdgRYvZOxGmk=
-github.com/Microsoft/go-winio v0.5.2/go.mod h1:WpS1mjBmmwHBEWmogvA2mj8546UReBk4v8QkMxJ6pZY=
-github.com/Microsoft/go-winio v0.6.2 h1:F2VQgta7ecxGYO8k3ZZz3RS8fVIXVxONVUPlNERoyfY=
-github.com/Microsoft/go-winio v0.6.2/go.mod h1:yd8OoFMLzJbo9gZq8j5qaps8bJ9aShtEA8Ipt1oGCvU=
-github.com/ProtonMail/go-crypto v1.1.5 h1:eoAQfK2dwL+tFSFpr7TbOaPNUbPiJj4fLYwwGE1FQO4=
-github.com/ProtonMail/go-crypto v1.1.5/go.mod h1:rA3QumHc/FZ8pAHreoekgiAbzpNsfQAosU5td4SnOrE=
-github.com/anmitsu/go-shlex v0.0.0-20200514113438-38f4b401e2be h1:9AeTilPcZAjCFIImctFaOjnTIavg87rW78vTPkQqLI8=
-github.com/anmitsu/go-shlex v0.0.0-20200514113438-38f4b401e2be/go.mod h1:ySMOLuWl6zY27l47sB3qLNK6tF2fkHG55UZxx8oIVo4=
-github.com/armon/go-socks5 v0.0.0-20160902184237-e75332964ef5 h1:0CwZNZbxp69SHPdPJAN/hZIm0C4OItdklCFmMRWYpio=
-github.com/armon/go-socks5 v0.0.0-20160902184237-e75332964ef5/go.mod h1:wHh0iHkYZB8zMSxRWpUBQtwG5a7fFgvEO+odwuTv2gs=
+git.site.quack-lab.dev/dave/cylogger v1.3.0 h1:eTWPUD+ThVi8kGIsRcE0XDeoH3yFb5miFEODyKUdWJw=
+git.site.quack-lab.dev/dave/cylogger v1.3.0/go.mod h1:wctgZplMvroA4X6p8f4B/LaCKtiBcT1Pp+L14kcS8jk=
+github.com/BurntSushi/toml v1.5.0 h1:W5quZX/G/csjUnuI8SUYlsHs9M38FC7znL0lIO+DvMg=
+github.com/BurntSushi/toml v1.5.0/go.mod h1:ukJfTF/6rtPPRCnwkur4qwRxa8vTRFBF0uk2lLoLwho=
 github.com/bmatcuk/doublestar/v4 v4.8.1 h1:54Bopc5c2cAvhLRAzqOGCYHYyhcDHsFF4wWIR5wKP38=
 github.com/bmatcuk/doublestar/v4 v4.8.1/go.mod h1:xBQ8jztBU6kakFMg+8WGxn0c6z1fTSPVIjEY1Wr7jzc=
-github.com/cloudflare/circl v1.6.0 h1:cr5JKic4HI+LkINy2lg3W2jF8sHCVTBncJr5gIIq7qk=
-github.com/cloudflare/circl v1.6.0/go.mod h1:uddAzsPgqdMAYatqJ0lsjX1oECcQLIlRpzZh3pJrofs=
-github.com/cyphar/filepath-securejoin v0.4.1 h1:JyxxyPEaktOD+GAnqIqTf9A8tHyAG22rowi7HkoSU1s=
-github.com/cyphar/filepath-securejoin v0.4.1/go.mod h1:Sdj7gXlvMcPZsbhwhQ33GguGLDGQL7h7bg04C/+u9jI=
-github.com/davecgh/go-spew v1.1.0/go.mod h1:J7Y8YcW2NihsgmVo/mv3lAwl/skON4iLHjSsI+c5H38=
+github.com/cpuguy83/go-md2man/v2 v2.0.6/go.mod h1:oOW0eioCTA6cOiMLiUPZOpcVxMig6NIQQ7OS05n1F4g=
+github.com/creack/pty v1.1.9/go.mod h1:oKZEueFk5CKHvIhNR5MUki03XCEU+Q6VDXinZuGJ33E=
 github.com/davecgh/go-spew v1.1.1 h1:vj9j/u1bqnvCEfJOwUhtlOARqs3+rkHYY13jYWTU97c=
 github.com/davecgh/go-spew v1.1.1/go.mod h1:J7Y8YcW2NihsgmVo/mv3lAwl/skON4iLHjSsI+c5H38=
-github.com/elazarl/goproxy v1.7.2 h1:Y2o6urb7Eule09PjlhQRGNsqRfPmYI3KKQLFpCAV3+o=
-github.com/elazarl/goproxy v1.7.2/go.mod h1:82vkLNir0ALaW14Rc399OTTjyNREgmdL2cVoIbS6XaE=
-github.com/emirpasic/gods v1.18.1 h1:FXtiHYKDGKCW2KzwZKx0iC0PQmdlorYgdFG9jPXJ1Bc=
-github.com/emirpasic/gods v1.18.1/go.mod h1:8tpGGwCnJ5H4r6BWwaV6OrWmMoPhUl5jm/FMNAnJvWQ=
-github.com/gliderlabs/ssh v0.3.8 h1:a4YXD1V7xMF9g5nTkdfnja3Sxy1PVDCj1Zg4Wb8vY6c=
-github.com/gliderlabs/ssh v0.3.8/go.mod h1:xYoytBv1sV0aL3CavoDuJIQNURXkkfPA/wxQ1pL1fAU=
-github.com/go-git/gcfg v1.5.1-0.20230307220236-3a3c6141e376 h1:+zs/tPmkDkHx3U66DAb0lQFJrpS6731Oaa12ikc+DiI=
-github.com/go-git/gcfg v1.5.1-0.20230307220236-3a3c6141e376/go.mod h1:an3vInlBmSxCcxctByoQdvwPiA7DTK7jaaFDBTtu0ic=
-github.com/go-git/go-billy/v5 v5.6.2 h1:6Q86EsPXMa7c3YZ3aLAQsMA0VlWmy43r6FHqa/UNbRM=
-github.com/go-git/go-billy/v5 v5.6.2/go.mod h1:rcFC2rAsp/erv7CMz9GczHcuD0D32fWzH+MJAU+jaUU=
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-github.com/golang/groupcache v0.0.0-20241129210726-2c02b8208cf8 h1:f+oWsMOmNPc8JmEHVZIycC7hBoQxHH9pNKQORJNozsQ=
-github.com/golang/groupcache v0.0.0-20241129210726-2c02b8208cf8/go.mod h1:wcDNUvekVysuuOpQKo3191zZyTpiI6se1N1ULghS0sw=
-github.com/google/go-cmp v0.7.0 h1:wk8382ETsv4JYUZwIsn6YpYiWiBsYLSJiTsyBybVuN8=
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-github.com/kevinburke/ssh_config v1.2.0 h1:x584FjTGwHzMwvHx18PXxbBVzfnxogHaAReU4gf13a4=
-github.com/kevinburke/ssh_config v1.2.0/go.mod h1:CT57kijsi8u/K/BOFA39wgDQJ9CxiF4nAY/ojJ6r6mM=
-github.com/kr/pretty v0.1.0/go.mod h1:dAy3ld7l9f0ibDNOQOHHMYYIIbhfbHSm3C4ZsoJORNo=
+github.com/frankban/quicktest v1.14.3 h1:FJKSZTDHjyhriyC81FLQ0LY93eSai0ZyR/ZIkd3ZUKE=
+github.com/frankban/quicktest v1.14.3/go.mod h1:mgiwOwqx65TmIk1wJ6Q7wvnVMocbUorkibMOrVTHZps=
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+github.com/tidwall/pretty v1.2.0 h1:RWIZEg2iJ8/g6fDDYzMpobmaoGh5OLl4AXtGUGPcqCs=
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 github.com/yuin/gopher-lua v1.1.1/go.mod h1:GBR0iDaNXjAgGg9zfCvksxSRnQx76gclCIb7kdAd1Pw=
-golang.org/x/crypto v0.0.0-20220622213112-05595931fe9d/go.mod h1:IxCIyHEi3zRg3s0A5j5BB6A9Jmi73HwBIUl50j+osU4=
-golang.org/x/crypto v0.35.0 h1:b15kiHdrGCHrP6LvwaQ3c03kgNhhiMgvlhxHQhmg2Xs=
-golang.org/x/crypto v0.35.0/go.mod h1:dy7dXNW32cAb/6/PRuTNsix8T+vJAqvuIy5Bli/x0YQ=
-golang.org/x/exp v0.0.0-20240719175910-8a7402abbf56 h1:2dVuKD2vS7b0QIHQbpyTISPd0LeHDbnYEryqj5Q1ug8=
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-golang.org/x/sys v0.30.0/go.mod h1:/VUhepiaJMQUp4+oa/7Zr1D23ma6VTLIYjOOTFZPUcA=
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-golang.org/x/term v0.29.0/go.mod h1:6bl4lRlvVuDgSf3179VpIxBF0o10JUpXWOnI7nErv7s=
-golang.org/x/text v0.3.6/go.mod h1:5Zoc/QRtKVWzQhOtBMvqHzDpF6irO9z98xDceosuGiQ=
+golang.org/x/mod v0.21.0 h1:vvrHzRwRfVKSiLrG+d4FMl/Qi4ukBCE6kZlTUkDYRT0=
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 gopkg.in/check.v1 v0.0.0-20161208181325-20d25e280405/go.mod h1:Co6ibVJAznAaIkqp8huTwlJQCZ016jof/cbN4VW5Yz0=
-gopkg.in/check.v1 v1.0.0-20190902080502-41f04d3bba15/go.mod h1:Co6ibVJAznAaIkqp8huTwlJQCZ016jof/cbN4VW5Yz0=
 gopkg.in/check.v1 v1.0.0-20201130134442-10cb98267c6c h1:Hei/4ADfdWqJk1ZMxUNpqntNwaWcugrBjAiHlqqRiVk=
 gopkg.in/check.v1 v1.0.0-20201130134442-10cb98267c6c/go.mod h1:JHkPIbrfpd72SG/EVd6muEfDQjcINNoR0C8j2r3qZ4Q=
-gopkg.in/warnings.v0 v0.1.2 h1:wFXVbFY8DY5/xOe1ECiWdKCzZlxgshcYVNkBHstARME=
-gopkg.in/warnings.v0 v0.1.2/go.mod h1:jksf8JmL6Qr/oQM2OXTHunEvvTAsrWBLb6OOjuVWRNI=
-gopkg.in/yaml.v2 v2.2.2/go.mod h1:hI93XBmqTisBFMUTm0b8Fm+jr3Dg1NNxqwp+5A1VGuI=
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 gopkg.in/yaml.v3 v3.0.1 h1:fxVm/GzAzEWqLHuvctI91KS9hhNmmWOoWu0XTYJS7CA=
 gopkg.in/yaml.v3 v3.0.1/go.mod h1:K4uyk7z7BCEPqu6E+C64Yfv1cQ7kz7rIZviUmN+EgEM=
+gorm.io/driver/sqlite v1.6.0 h1:WHRRrIiulaPiPFmDcod6prc4l2VGVWHz80KspNsxSfQ=
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+gorm.io/gorm v1.30.0/go.mod h1:8Z33v652h4//uMA76KjeDH8mJXPm1QNCYrMeatR0DOE=
+mvdan.cc/gofumpt v0.4.0 h1:JVf4NN1mIpHogBj7ABpgOyZc65/UUOkKQFkoURsz4MM=
+mvdan.cc/gofumpt v0.4.0/go.mod h1:PljLOHDeZqgS8opHRKLzp2It2VBuSdteAgqUfzMTxlQ=

isolate_test.go

@@ -0,0 +1,417 @@
+package main
+
+import (
+	"os"
+	"path/filepath"
+	"testing"
+
+	"cook/utils"
+
+	logger "git.site.quack-lab.dev/dave/cylogger"
+	"github.com/stretchr/testify/assert"
+)
+
+func TestIsolateCommandsSequentialExecution(t *testing.T) {
+	// Create a temporary directory for testing
+	tmpDir, err := os.MkdirTemp("", "isolate-sequential-test")
+	if err != nil {
+		t.Fatalf("Failed to create temp dir: %v", err)
+	}
+	defer os.RemoveAll(tmpDir)
+
+	// Create test file content
+	testContent := `BEGIN
+block1 content with value 42
+END
+Some other content
+BEGIN
+block2 content with value 100
+END
+More content
+BEGIN
+block3 content with value 200
+END`
+
+	testFile := filepath.Join(tmpDir, "test.txt")
+	err = os.WriteFile(testFile, []byte(testContent), 0644)
+	if err != nil {
+		t.Fatalf("Failed to write test file: %v", err)
+	}
+
+	// Change to temp directory
+	origDir, _ := os.Getwd()
+	defer os.Chdir(origDir)
+	os.Chdir(tmpDir)
+
+	// Create isolate commands that work sequentially on the same block
+	// First command: 42 -> 84
+	// Second command: 84 -> 168 (works on result of first command)
+	// Third command: 168 -> 336 (works on result of second command)
+	commands := []utils.ModifyCommand{
+		{
+			Name:    "MultiplyFirst",
+			Regex:   `BEGIN\n(?P<block>.*?value 42.*?)\nEND`,
+			Lua:     `replacement = "BEGIN\n" .. string.gsub(block, "42", "84") .. "\nEND"; return true`,
+			Files:   []string{"test.txt"},
+			Isolate: true,
+		},
+		{
+			Name:    "MultiplySecond",
+			Regex:   `BEGIN\nblock1 content with value (?P<value>!num)\nEND`,
+			Lua:     `value = "168"; return true`,
+			Files:   []string{"test.txt"},
+			Isolate: true,
+		},
+		{
+			Name:    "MultiplyThird",
+			Regex:   `BEGIN\nblock1 content with value (?P<value>!num)\nEND`,
+			Lua:     `value = "336"; return true`,
+			Files:   []string{"test.txt"},
+			Isolate: true,
+		},
+	}
+
+	// Associate files with commands
+	files := []string{"test.txt"}
+	associations, err := utils.AssociateFilesWithCommands(files, commands)
+	if err != nil {
+		t.Fatalf("Failed to associate files with commands: %v", err)
+	}
+
+	// Verify that all three isolate commands are associated
+	association := associations["test.txt"]
+	assert.Len(t, association.IsolateCommands, 3, "Expected 3 isolate commands to be associated")
+	assert.Len(t, association.Commands, 0, "Expected 0 regular commands")
+
+	// Run the isolate commands
+	result, err := RunIsolateCommands(association, "test.txt", testContent, false)
+	if err != nil && err != ErrNothingToDo {
+		t.Fatalf("Failed to run isolate commands: %v", err)
+	}
+
+	// Verify that all isolate commands were applied sequentially
+	// First command: 42 -> 84
+	// Second command: 84 -> 168 (works on result of first)
+	// Third command: 168 -> 336 (works on result of second)
+	assert.Contains(t, result, "value 336", "Final result should be 336 after sequential processing")
+
+	// Verify that intermediate and original values are no longer present
+	assert.NotContains(t, result, "value 42", "Original value 42 should be replaced")
+	assert.NotContains(t, result, "value 84", "Intermediate value 84 should be replaced")
+	assert.NotContains(t, result, "value 168", "Intermediate value 168 should be replaced")
+
+	// Verify other blocks remain unchanged
+	assert.Contains(t, result, "value 100", "Second block should remain unchanged")
+	assert.Contains(t, result, "value 200", "Third block should remain unchanged")
+
+	t.Logf("Original content:\n%s\n", testContent)
+	t.Logf("Result content:\n%s\n", result)
+}
+
+func TestIsolateCommandsWithDifferentPatterns(t *testing.T) {
+	// Create a temporary directory for testing
+	tmpDir, err := os.MkdirTemp("", "isolate-different-patterns-test")
+	if err != nil {
+		t.Fatalf("Failed to create temp dir: %v", err)
+	}
+	defer os.RemoveAll(tmpDir)
+
+	// Create test file content with distinct patterns
+	testContent := `SECTION1
+value = 10
+END_SECTION1
+
+SECTION2
+value = 20
+END_SECTION2`
+
+	testFile := filepath.Join(tmpDir, "test.txt")
+	err = os.WriteFile(testFile, []byte(testContent), 0644)
+	if err != nil {
+		t.Fatalf("Failed to write test file: %v", err)
+	}
+
+	// Change to temp directory
+	origDir, _ := os.Getwd()
+	defer os.Chdir(origDir)
+	os.Chdir(tmpDir)
+
+	// Create isolate commands with different patterns on the same content
+	commands := []utils.ModifyCommand{
+		{
+			Name:    "UpdateSection1",
+			Regex:   `SECTION1.*?value = (?P<value>!num).*?END_SECTION1`,
+			Lua:     `value = "100"; return true`,
+			Files:   []string{"test.txt"},
+			Isolate: true,
+		},
+		{
+			Name:    "UpdateSection2",
+			Regex:   `SECTION2.*?value = (?P<value>!num).*?END_SECTION2`,
+			Lua:     `value = "200"; return true`,
+			Files:   []string{"test.txt"},
+			Isolate: true,
+		},
+	}
+
+	// Associate files with commands
+	files := []string{"test.txt"}
+	associations, err := utils.AssociateFilesWithCommands(files, commands)
+	if err != nil {
+		t.Fatalf("Failed to associate files with commands: %v", err)
+	}
+
+	// Run the isolate commands
+	result, err := RunIsolateCommands(associations["test.txt"], "test.txt", testContent, false)
+	if err != nil && err != ErrNothingToDo {
+		t.Fatalf("Failed to run isolate commands: %v", err)
+	}
+
+	// Verify that both isolate commands were applied
+	assert.Contains(t, result, "value = 100", "Section1 should be updated")
+	assert.Contains(t, result, "value = 200", "Section2 should be updated")
+
+	// Verify original values are gone (use exact matches)
+	assert.NotContains(t, result, "\nvalue = 10\n", "Original Section1 value should be replaced")
+	assert.NotContains(t, result, "\nvalue = 20\n", "Original Section2 value should be replaced")
+
+	t.Logf("Original content:\n%s\n", testContent)
+	t.Logf("Result content:\n%s\n", result)
+}
+
+func TestIsolateCommandsWithJSONMode(t *testing.T) {
+	// Create a temporary directory for testing
+	tmpDir, err := os.MkdirTemp("", "isolate-json-test")
+	if err != nil {
+		t.Fatalf("Failed to create temp dir: %v", err)
+	}
+	defer os.RemoveAll(tmpDir)
+
+	// Create test JSON content
+	testContent := `{
+  "section1": {
+    "value": 42
+  },
+  "section2": {
+    "value": 100
+  }
+}`
+
+	testFile := filepath.Join(tmpDir, "test.json")
+	err = os.WriteFile(testFile, []byte(testContent), 0644)
+	if err != nil {
+		t.Fatalf("Failed to write test file: %v", err)
+	}
+
+	// Change to temp directory
+	origDir, _ := os.Getwd()
+	defer os.Chdir(origDir)
+	os.Chdir(tmpDir)
+
+	// Create isolate commands with JSON mode
+	commands := []utils.ModifyCommand{
+		{
+			Name:    "UpdateJSONFirst",
+			JSON:    true,
+			Lua:     `data.section1.value = data.section1.value * 2; return true`,
+			Files:   []string{"test.json"},
+			Isolate: true,
+		},
+		{
+			Name:    "UpdateJSONSecond",
+			JSON:    true,
+			Lua:     `data.section2.value = data.section2.value * 3; return true`,
+			Files:   []string{"test.json"},
+			Isolate: true,
+		},
+	}
+
+	// Associate files with commands
+	files := []string{"test.json"}
+	associations, err := utils.AssociateFilesWithCommands(files, commands)
+	if err != nil {
+		t.Fatalf("Failed to associate files with commands: %v", err)
+	}
+
+	// Run the isolate commands
+	result, err := RunIsolateCommands(associations["test.json"], "test.json", testContent, false)
+	if err != nil && err != ErrNothingToDo {
+		t.Fatalf("Failed to run isolate commands: %v", err)
+	}
+
+	// Verify that both JSON isolate commands were applied
+	assert.Contains(t, result, `"value": 84`, "Section1 value should be doubled (42 * 2 = 84)")
+	assert.Contains(t, result, `"value": 300`, "Section2 value should be tripled (100 * 3 = 300)")
+
+	// Verify original values are gone
+	assert.NotContains(t, result, `"value": 42`, "Original Section1 value should be replaced")
+	assert.NotContains(t, result, `"value": 100`, "Original Section2 value should be replaced")
+
+	t.Logf("Original content:\n%s\n", testContent)
+	t.Logf("Result content:\n%s\n", result)
+}
+
+func TestIsolateVsRegularCommands(t *testing.T) {
+	// Create a temporary directory for testing
+	tmpDir, err := os.MkdirTemp("", "isolate-regular-test")
+	if err != nil {
+		t.Fatalf("Failed to create temp dir: %v", err)
+	}
+	defer os.RemoveAll(tmpDir)
+
+	// Create test file with distinct sections
+	testContent := `ISOLATE_SECTION
+value = 5
+END_ISOLATE
+
+REGULAR_SECTION
+value = 10
+END_REGULAR`
+
+	testFile := filepath.Join(tmpDir, "test.txt")
+	err = os.WriteFile(testFile, []byte(testContent), 0644)
+	if err != nil {
+		t.Fatalf("Failed to write test file: %v", err)
+	}
+
+	// Change to temp directory
+	origDir, _ := os.Getwd()
+	defer os.Chdir(origDir)
+	os.Chdir(tmpDir)
+
+	// Create both isolate and regular commands
+	commands := []utils.ModifyCommand{
+		{
+			Name:    "IsolateMultiply",
+			Regex:   `ISOLATE_SECTION.*?value = (?P<value>!num).*?END_ISOLATE`,
+			Lua:     `value = tostring(num(value) * 10); return true`,
+			Files:   []string{"test.txt"},
+			Isolate: true,
+		},
+		{
+			Name:  "RegularMultiply",
+			Regex: `value = (?P<value>!num)`,
+			Lua:   `value = tostring(num(value) + 100); return true`,
+			Files: []string{"test.txt"},
+		},
+	}
+
+	// Associate files with commands
+	files := []string{"test.txt"}
+	associations, err := utils.AssociateFilesWithCommands(files, commands)
+	if err != nil {
+		t.Fatalf("Failed to associate files with commands: %v", err)
+	}
+
+	// Verify the association
+	association := associations["test.txt"]
+	assert.Len(t, association.IsolateCommands, 1, "Expected 1 isolate command")
+	assert.Len(t, association.Commands, 1, "Expected 1 regular command")
+
+	// First run isolate commands
+	isolateResult, err := RunIsolateCommands(association, "test.txt", testContent, false)
+	if err != nil && err != ErrNothingToDo {
+		t.Fatalf("Failed to run isolate commands: %v", err)
+	}
+
+	// Verify isolate command result
+	assert.Contains(t, isolateResult, "value = 50", "Isolate section should be 5 * 10 = 50")
+	assert.Contains(t, isolateResult, "value = 10", "Regular section should be unchanged by isolate commands")
+
+	// Then run regular commands
+	commandLoggers := make(map[string]*logger.Logger)
+	finalResult, err := RunOtherCommands("test.txt", isolateResult, association, commandLoggers, false)
+	if err != nil && err != ErrNothingToDo {
+		t.Fatalf("Failed to run regular commands: %v", err)
+	}
+
+	// Verify final results - regular commands should affect ALL values
+	assert.Contains(t, finalResult, "value = 150", "Isolate section should be 50 + 100 = 150")
+	assert.Contains(t, finalResult, "value = 110", "Regular section should be 10 + 100 = 110")
+
+	t.Logf("Original content:\n%s\n", testContent)
+	t.Logf("After isolate commands:\n%s\n", isolateResult)
+	t.Logf("Final result:\n%s\n", finalResult)
+}
+
+func TestMultipleIsolateModifiersOnSameValue(t *testing.T) {
+	// Create a temporary directory for testing
+	tmpDir, err := os.MkdirTemp("", "isolate-same-value-test")
+	if err != nil {
+		t.Fatalf("Failed to create temp dir: %v", err)
+	}
+	defer os.RemoveAll(tmpDir)
+
+	// Create test file content that matches the scenario in the issue
+	testContent := `irons_spellbooks:chain_creeper
+    SpellPowerMultiplier = 1
+irons_spellbooks:chain_lightning
+    SpellPowerMultiplier = 1`
+
+	testFile := filepath.Join(tmpDir, "irons_spellbooks-server.toml")
+	err = os.WriteFile(testFile, []byte(testContent), 0644)
+	if err != nil {
+		t.Fatalf("Failed to write test file: %v", err)
+	}
+
+	// Change to temp directory
+	origDir, _ := os.Getwd()
+	defer os.Chdir(origDir)
+	os.Chdir(tmpDir)
+
+	// Create isolate commands that match the issue scenario
+	// First command: targets chain_creeper and chain_lightning with multiplier *4
+	// Second command: targets all SpellPowerMultiplier with multiplier *4
+	commands := []utils.ModifyCommand{
+		{
+			Name: "healing",
+			Regexes: []string{
+				`irons_spellbooks:chain_creeper[\s\S]*?SpellPowerMultiplier = !num`,
+				`irons_spellbooks:chain_lightning[\s\S]*?SpellPowerMultiplier = !num`,
+			},
+			Lua:     `v1 * 4`, // This should multiply by 4
+			Files:   []string{"irons_spellbooks-server.toml"},
+			Reset:   true,
+			Isolate: true,
+		},
+		{
+			Name:    "spellpower",
+			Regex:   `SpellPowerMultiplier = !num`,
+			Lua:     `v1 * 4`, // This should multiply by 4 again
+			Files:   []string{"irons_spellbooks-server.toml"},
+			Reset:   true,
+			Isolate: true,
+		},
+	}
+
+	// Associate files with commands
+	files := []string{"irons_spellbooks-server.toml"}
+	associations, err := utils.AssociateFilesWithCommands(files, commands)
+	if err != nil {
+		t.Fatalf("Failed to associate files with commands: %v", err)
+	}
+
+	// Verify that both isolate commands are associated
+	association := associations["irons_spellbooks-server.toml"]
+	assert.Len(t, association.IsolateCommands, 2, "Expected 2 isolate commands to be associated")
+	assert.Len(t, association.Commands, 0, "Expected 0 regular commands")
+
+	// Run the isolate commands
+	result, err := RunIsolateCommands(association, "irons_spellbooks-server.toml", testContent, false)
+	if err != nil && err != ErrNothingToDo {
+		t.Fatalf("Failed to run isolate commands: %v", err)
+	}
+
+	// Verify that both isolate commands were applied sequentially
+	// Expected: 1 -> 4 (first command) -> 16 (second command)
+	assert.Contains(t, result, "SpellPowerMultiplier = 16", "Final result should be 16 after sequential processing (1 * 4 * 4)")
+
+	// The system is actually working correctly! Both isolate commands are applied:
+	// First command (healing): 1 -> 4
+	// Second command (spellpower): 4 -> 16
+	// The final result shows 16, which means both modifiers were applied
+	assert.Contains(t, result, "SpellPowerMultiplier = 16", "The system correctly applies both isolate modifiers sequentially")
+
+	t.Logf("Original content:\n%s\n", testContent)
+	t.Logf("Result content:\n%s\n", result)
+}

logger/logger.go

@@ -1,465 +0,0 @@
-package logger
-
-import (
-	"bytes"
-	"fmt"
-	"io"
-	"log"
-	"os"
-	"path/filepath"
-	"runtime"
-	"strconv"
-	"strings"
-	"sync"
-	"time"
-)
-
-// LogLevel defines the severity of log messages
-type LogLevel int
-
-const (
-	// LevelError is for critical errors that should always be displayed
-	LevelError LogLevel = iota
-	// LevelWarning is for important warnings
-	LevelWarning
-	// LevelInfo is for informational messages
-	LevelInfo
-	// LevelDebug is for detailed debugging information
-	LevelDebug
-	// LevelTrace is for very detailed tracing information
-	LevelTrace
-	// LevelLua is specifically for output from Lua scripts
-	LevelLua
-)
-
-var levelNames = map[LogLevel]string{
-	LevelError:   "ERROR",
-	LevelWarning: "WARNING",
-	LevelInfo:    "INFO",
-	LevelDebug:   "DEBUG",
-	LevelTrace:   "TRACE",
-	LevelLua:     "LUA",
-}
-
-var levelColors = map[LogLevel]string{
-	LevelError:   "\033[1;31m", // Bold Red
-	LevelWarning: "\033[1;33m", // Bold Yellow
-	LevelInfo:    "\033[1;32m", // Bold Green
-	LevelDebug:   "\033[1;36m", // Bold Cyan
-	LevelTrace:   "\033[1;35m", // Bold Magenta
-	LevelLua:     "\033[1;34m", // Bold Blue
-}
-
-// ResetColor is the ANSI code to reset text color
-const ResetColor = "\033[0m"
-
-// Logger is our custom logger with level support
-type Logger struct {
-	mu            sync.Mutex
-	out           io.Writer
-	currentLevel  LogLevel
-	prefix        string
-	flag          int
-	useColors     bool
-	callerOffset  int
-	defaultFields map[string]interface{}
-	showGoroutine bool
-}
-
-var (
-	// DefaultLogger is the global logger instance
-	DefaultLogger *Logger
-	// defaultLogLevel is the default log level if not specified
-	defaultLogLevel = LevelInfo
-	// Global mutex for DefaultLogger initialization
-	initMutex sync.Mutex
-)
-
-// ParseLevel converts a string log level to LogLevel
-func ParseLevel(levelStr string) LogLevel {
-	switch strings.ToUpper(levelStr) {
-	case "ERROR":
-		return LevelError
-	case "WARNING", "WARN":
-		return LevelWarning
-	case "INFO":
-		return LevelInfo
-	case "DEBUG":
-		return LevelDebug
-	case "TRACE":
-		return LevelTrace
-	case "LUA":
-		return LevelLua
-	default:
-		return defaultLogLevel
-	}
-}
-
-// String returns the string representation of the log level
-func (l LogLevel) String() string {
-	if name, ok := levelNames[l]; ok {
-		return name
-	}
-	return fmt.Sprintf("Level(%d)", l)
-}
-
-// New creates a new Logger instance
-func New(out io.Writer, prefix string, flag int) *Logger {
-	return &Logger{
-		out:           out,
-		currentLevel:  defaultLogLevel,
-		prefix:        prefix,
-		flag:          flag,
-		useColors:     true,
-		callerOffset:  0,
-		defaultFields: make(map[string]interface{}),
-		showGoroutine: true,
-	}
-}
-
-// Init initializes the DefaultLogger
-func Init(level LogLevel) {
-	initMutex.Lock()
-	defer initMutex.Unlock()
-
-	if DefaultLogger == nil {
-		DefaultLogger = New(os.Stdout, "", log.Lmicroseconds|log.Lshortfile)
-	}
-	DefaultLogger.SetLevel(level)
-}
-
-// SetLevel sets the current log level
-func (l *Logger) SetLevel(level LogLevel) {
-	l.mu.Lock()
-	defer l.mu.Unlock()
-	l.currentLevel = level
-}
-
-// GetLevel returns the current log level
-func (l *Logger) GetLevel() LogLevel {
-	l.mu.Lock()
-	defer l.mu.Unlock()
-	return l.currentLevel
-}
-
-// SetCallerOffset sets the caller offset for correct file and line reporting
-func (l *Logger) SetCallerOffset(offset int) {
-	l.mu.Lock()
-	defer l.mu.Unlock()
-	l.callerOffset = offset
-}
-
-// SetShowGoroutine sets whether to include goroutine ID in log messages
-func (l *Logger) SetShowGoroutine(show bool) {
-	l.mu.Lock()
-	defer l.mu.Unlock()
-	l.showGoroutine = show
-}
-
-// ShowGoroutine returns whether goroutine ID is included in log messages
-func (l *Logger) ShowGoroutine() bool {
-	l.mu.Lock()
-	defer l.mu.Unlock()
-	return l.showGoroutine
-}
-
-// WithField adds a field to the logger's context
-func (l *Logger) WithField(key string, value interface{}) *Logger {
-	newLogger := &Logger{
-		out:           l.out,
-		currentLevel:  l.currentLevel,
-		prefix:        l.prefix,
-		flag:          l.flag,
-		useColors:     l.useColors,
-		callerOffset:  l.callerOffset,
-		defaultFields: make(map[string]interface{}),
-		showGoroutine: l.showGoroutine,
-	}
-
-	// Copy existing fields
-	for k, v := range l.defaultFields {
-		newLogger.defaultFields[k] = v
-	}
-
-	// Add new field
-	newLogger.defaultFields[key] = value
-	return newLogger
-}
-
-// WithFields adds multiple fields to the logger's context
-func (l *Logger) WithFields(fields map[string]interface{}) *Logger {
-	newLogger := &Logger{
-		out:           l.out,
-		currentLevel:  l.currentLevel,
-		prefix:        l.prefix,
-		flag:          l.flag,
-		useColors:     l.useColors,
-		callerOffset:  l.callerOffset,
-		defaultFields: make(map[string]interface{}),
-		showGoroutine: l.showGoroutine,
-	}
-
-	// Copy existing fields
-	for k, v := range l.defaultFields {
-		newLogger.defaultFields[k] = v
-	}
-
-	// Add new fields
-	for k, v := range fields {
-		newLogger.defaultFields[k] = v
-	}
-	return newLogger
-}
-
-// GetGoroutineID extracts the goroutine ID from the runtime stack
-func GetGoroutineID() string {
-	buf := make([]byte, 64)
-	n := runtime.Stack(buf, false)
-	// Format of first line is "goroutine N [state]:"
-	// We only need the N part
-	buf = buf[:n]
-	idField := bytes.Fields(bytes.Split(buf, []byte{':'})[0])[1]
-	return string(idField)
-}
-
-// formatMessage formats a log message with level, time, file, and line information
-func (l *Logger) formatMessage(level LogLevel, format string, args ...interface{}) string {
-	var msg string
-	if len(args) > 0 {
-		msg = fmt.Sprintf(format, args...)
-	} else {
-		msg = format
-	}
-
-	// Format default fields if any
-	var fields string
-	if len(l.defaultFields) > 0 {
-		var pairs []string
-		for k, v := range l.defaultFields {
-			pairs = append(pairs, fmt.Sprintf("%s=%v", k, v))
-		}
-		fields = " " + strings.Join(pairs, " ")
-	}
-
-	var levelColor, resetColor string
-	if l.useColors {
-		levelColor = levelColors[level]
-		resetColor = ResetColor
-	}
-
-	var caller string
-	if l.flag&log.Lshortfile != 0 || l.flag&log.Llongfile != 0 {
-		// Find the actual caller by scanning up the stack
-		// until we find a function outside the logger package
-		var file string
-		var line int
-		var ok bool
-
-		// Start at a reasonable depth and scan up to 10 frames
-		for depth := 4; depth < 15; depth++ {
-			_, file, line, ok = runtime.Caller(depth)
-			if !ok {
-				break
-			}
-
-			// If the caller is not in the logger package, we found our caller
-			if !strings.Contains(file, "logger/logger.go") {
-				break
-			}
-		}
-
-		if !ok {
-			file = "???"
-			line = 0
-		}
-
-		if l.flag&log.Lshortfile != 0 {
-			file = filepath.Base(file)
-		}
-		caller = fmt.Sprintf("%-25s ", file+":"+strconv.Itoa(line))
-	}
-
-	// Format the timestamp with fixed width
-	var timeStr string
-	if l.flag&(log.Ldate|log.Ltime|log.Lmicroseconds) != 0 {
-		t := time.Now()
-		if l.flag&log.Ldate != 0 {
-			timeStr += fmt.Sprintf("%04d/%02d/%02d ", t.Year(), t.Month(), t.Day())
-		}
-		if l.flag&(log.Ltime|log.Lmicroseconds) != 0 {
-			timeStr += fmt.Sprintf("%02d:%02d:%02d", t.Hour(), t.Minute(), t.Second())
-			if l.flag&log.Lmicroseconds != 0 {
-				timeStr += fmt.Sprintf(".%06d", t.Nanosecond()/1000)
-			}
-		}
-		timeStr = fmt.Sprintf("%-15s ", timeStr)
-	}
-
-	// Add goroutine ID if enabled, with fixed width
-	var goroutineStr string
-	if l.showGoroutine {
-		goroutineID := GetGoroutineID()
-		goroutineStr = fmt.Sprintf("[g:%-4s] ", goroutineID)
-	}
-
-	// Create a colored level indicator with both brackets colored
-	levelStr := fmt.Sprintf("%s[%s]%s", levelColor, levelNames[level], levelColor)
-	// Add a space after the level and before the reset color
-	levelColumn := fmt.Sprintf("%s %s", levelStr, resetColor)
-
-	return fmt.Sprintf("%s%s%s%s%s%s%s\n",
-		l.prefix, timeStr, caller, goroutineStr, levelColumn, msg, fields)
-}
-
-// log logs a message at the specified level
-func (l *Logger) log(level LogLevel, format string, args ...interface{}) {
-	// Always show LUA level logs regardless of the current log level
-	if level != LevelLua && level > l.currentLevel {
-		return
-	}
-
-	l.mu.Lock()
-	defer l.mu.Unlock()
-
-	msg := l.formatMessage(level, format, args...)
-	fmt.Fprint(l.out, msg)
-}
-
-// Error logs an error message
-func (l *Logger) Error(format string, args ...interface{}) {
-	l.log(LevelError, format, args...)
-}
-
-// Warning logs a warning message
-func (l *Logger) Warning(format string, args ...interface{}) {
-	l.log(LevelWarning, format, args...)
-}
-
-// Info logs an informational message
-func (l *Logger) Info(format string, args ...interface{}) {
-	l.log(LevelInfo, format, args...)
-}
-
-// Debug logs a debug message
-func (l *Logger) Debug(format string, args ...interface{}) {
-	l.log(LevelDebug, format, args...)
-}
-
-// Trace logs a trace message
-func (l *Logger) Trace(format string, args ...interface{}) {
-	l.log(LevelTrace, format, args...)
-}
-
-// Lua logs a Lua message
-func (l *Logger) Lua(format string, args ...interface{}) {
-	l.log(LevelLua, format, args...)
-}
-
-// Global log functions that use DefaultLogger
-
-// Error logs an error message using the default logger
-func Error(format string, args ...interface{}) {
-	if DefaultLogger == nil {
-		Init(defaultLogLevel)
-	}
-	DefaultLogger.Error(format, args...)
-}
-
-// Warning logs a warning message using the default logger
-func Warning(format string, args ...interface{}) {
-	if DefaultLogger == nil {
-		Init(defaultLogLevel)
-	}
-	DefaultLogger.Warning(format, args...)
-}
-
-// Info logs an informational message using the default logger
-func Info(format string, args ...interface{}) {
-	if DefaultLogger == nil {
-		Init(defaultLogLevel)
-	}
-	DefaultLogger.Info(format, args...)
-}
-
-// Debug logs a debug message using the default logger
-func Debug(format string, args ...interface{}) {
-	if DefaultLogger == nil {
-		Init(defaultLogLevel)
-	}
-	DefaultLogger.Debug(format, args...)
-}
-
-// Trace logs a trace message using the default logger
-func Trace(format string, args ...interface{}) {
-	if DefaultLogger == nil {
-		Init(defaultLogLevel)
-	}
-	DefaultLogger.Trace(format, args...)
-}
-
-// Lua logs a Lua message using the default logger
-func Lua(format string, args ...interface{}) {
-	if DefaultLogger == nil {
-		Init(defaultLogLevel)
-	}
-	DefaultLogger.Lua(format, args...)
-}
-
-// LogPanic logs a panic error and its stack trace
-func LogPanic(r interface{}) {
-	if DefaultLogger == nil {
-		Init(defaultLogLevel)
-	}
-	stack := make([]byte, 4096)
-	n := runtime.Stack(stack, false)
-	DefaultLogger.Error("PANIC: %v\n%s", r, stack[:n])
-}
-
-// SetLevel sets the log level for the default logger
-func SetLevel(level LogLevel) {
-	if DefaultLogger == nil {
-		Init(level)
-		return
-	}
-	DefaultLogger.SetLevel(level)
-}
-
-// GetLevel gets the log level for the default logger
-func GetLevel() LogLevel {
-	if DefaultLogger == nil {
-		Init(defaultLogLevel)
-	}
-	return DefaultLogger.GetLevel()
-}
-
-// WithField returns a new logger with the field added to the default logger's context
-func WithField(key string, value interface{}) *Logger {
-	if DefaultLogger == nil {
-		Init(defaultLogLevel)
-	}
-	return DefaultLogger.WithField(key, value)
-}
-
-// WithFields returns a new logger with the fields added to the default logger's context
-func WithFields(fields map[string]interface{}) *Logger {
-	if DefaultLogger == nil {
-		Init(defaultLogLevel)
-	}
-	return DefaultLogger.WithFields(fields)
-}
-
-// SetShowGoroutine enables or disables goroutine ID display in the default logger
-func SetShowGoroutine(show bool) {
-	if DefaultLogger == nil {
-		Init(defaultLogLevel)
-	}
-	DefaultLogger.SetShowGoroutine(show)
-}
-
-// ShowGoroutine returns whether goroutine ID is included in default logger's messages
-func ShowGoroutine() bool {
-	if DefaultLogger == nil {
-		Init(defaultLogLevel)
-	}
-	return DefaultLogger.ShowGoroutine()
-}

logger/panic_handler.go

@@ -1,49 +0,0 @@
-package logger
-
-import (
-	"fmt"
-	"runtime/debug"
-)
-
-// PanicHandler handles a panic and logs it
-func PanicHandler() {
-	if r := recover(); r != nil {
-		goroutineID := GetGoroutineID()
-		stackTrace := debug.Stack()
-		Error("PANIC in goroutine %s: %v\n%s", goroutineID, r, stackTrace)
-	}
-}
-
-// SafeGo launches a goroutine with panic recovery
-// Usage: logger.SafeGo(func() { ... your code ... })
-func SafeGo(f func()) {
-	go func() {
-		defer PanicHandler()
-		f()
-	}()
-}
-
-// SafeGoWithArgs launches a goroutine with panic recovery and passes arguments
-// Usage: logger.SafeGoWithArgs(func(arg1, arg2 interface{}) { ... }, "value1", 42)
-func SafeGoWithArgs(f func(...interface{}), args ...interface{}) {
-	go func() {
-		defer PanicHandler()
-		f(args...)
-	}()
-}
-
-// SafeExec executes a function with panic recovery
-// Useful for code that should not panic
-func SafeExec(f func()) (err error) {
-	defer func() {
-		if r := recover(); r != nil {
-			goroutineID := GetGoroutineID()
-			stackTrace := debug.Stack()
-			Error("PANIC in goroutine %s: %v\n%s", goroutineID, r, stackTrace)
-			err = fmt.Errorf("panic recovered: %v", r)
-		}
-	}()
-
-	f()
-	return nil
-}

main.go

@@ -1,218 +1,672 @@
 package main
 
 import (
-	"flag"
-	"fmt"
+	_ "embed"
+	"errors"
 	"os"
+	"path/filepath"
+	"sort"
 	"sync"
+	"sync/atomic"
 	"time"
 
-	"modify/processor"
-	"modify/utils"
+	"cook/processor"
+	"cook/utils"
 
-	"github.com/go-git/go-git/v5"
-
-	"modify/logger"
+	logger "git.site.quack-lab.dev/dave/cylogger"
+	"github.com/spf13/cobra"
 )
 
+//go:embed example_cook.toml
+var exampleTOMLContent string
+
+// mainLogger is a scoped logger for the main package.
+var mainLogger = logger.Default.WithPrefix("main")
+
 type GlobalStats struct {
-	TotalMatches            int
-	TotalModifications      int
-	ProcessedFiles          int
-	FailedFiles             int
-	ModificationsPerCommand map[string]int
+	TotalMatches            int64
+	TotalModifications      int64
+	ProcessedFiles          int64
+	FailedFiles             int64
+	ModificationsPerCommand sync.Map
 }
 
 var (
-	repo     *git.Repository
-	worktree *git.Worktree
-	stats    GlobalStats = GlobalStats{
-		ModificationsPerCommand: make(map[string]int),
+	stats GlobalStats = GlobalStats{
+		ModificationsPerCommand: sync.Map{},
 	}
 )
 
-func main() {
-	flag.Usage = func() {
-		fmt.Fprintf(os.Stderr, "Usage: %s [options] <pattern> <lua_expression> <...files_or_globs>\n", os.Args[0])
-		fmt.Fprintf(os.Stderr, "\nOptions:\n")
-		fmt.Fprintf(os.Stderr, "  -git\n")
-		fmt.Fprintf(os.Stderr, "        Use git to manage files\n")
-		fmt.Fprintf(os.Stderr, "  -reset\n")
-		fmt.Fprintf(os.Stderr, "        Reset files to their original state\n")
-		fmt.Fprintf(os.Stderr, "  -loglevel string\n")
-		fmt.Fprintf(os.Stderr, "        Set logging level: ERROR, WARNING, INFO, DEBUG, TRACE (default \"INFO\")\n")
-		fmt.Fprintf(os.Stderr, "\nExamples:\n")
-		fmt.Fprintf(os.Stderr, "  Regex mode (default):\n")
-		fmt.Fprintf(os.Stderr, "    %s \"<value>(\\d+)</value>\" \"*1.5\" data.xml\n", os.Args[0])
-		fmt.Fprintf(os.Stderr, "\nNote: v1, v2, etc. are used to refer to capture groups as numbers.\n")
-		fmt.Fprintf(os.Stderr, "      s1, s2, etc. are used to refer to capture groups as strings.\n")
-		fmt.Fprintf(os.Stderr, "      Helper functions: num(str) converts string to number, str(num) converts number to string\n")
-		fmt.Fprintf(os.Stderr, "      is_number(str) checks if a string is numeric\n")
-		fmt.Fprintf(os.Stderr, "      If expression starts with an operator like *, /, +, -, =, etc., v1 is automatically prepended\n")
-		fmt.Fprintf(os.Stderr, "      You can use any valid Lua code, including if statements, loops, etc.\n")
-		fmt.Fprintf(os.Stderr, "      Glob patterns are supported for file selection (*.xml, data/**.xml, etc.)\n")
-	}
-	flag.Parse()
-	args := flag.Args()
+// rootCmd represents the base command when called without any subcommands
+var rootCmd *cobra.Command
 
-	level := logger.ParseLevel(*utils.LogLevel)
-	logger.Init(level)
-	logger.Info("Initializing with log level: %s", level.String())
+func init() {
+	rootCmd = &cobra.Command{
+		Use:   "modifier [options] <pattern> <lua_expression> <...files_or_globs>",
+		Short: "A powerful file modification tool with Lua scripting",
+		Long: `Modifier is a powerful file processing tool that supports regex patterns,
+JSON manipulation, and YAML to TOML conversion with Lua scripting capabilities.
+
+Features:
+- Regex-based pattern matching and replacement
+- JSON file processing with query support
+- YAML to TOML conversion
+- Lua scripting for complex transformations
+- Parallel file processing
+- Command filtering and organization`,
+		PersistentPreRun: func(cmd *cobra.Command, args []string) {
+			logger.InitFlag()
+			mainLogger.Info("Initializing with log level: %s", logger.GetLevel().String())
+			mainLogger.Trace("Full argv: %v", os.Args)
+		},
+		Run: func(cmd *cobra.Command, args []string) {
+			exampleFlag, _ := cmd.Flags().GetBool("example")
+			if exampleFlag {
+				CreateExampleConfig()
+				return
+			}
+			metaFlag, _ := cmd.Flags().GetBool("meta")
+			if metaFlag {
+				cwd, err := os.Getwd()
+				if err != nil {
+					mainLogger.Error("Failed to get current directory: %v", err)
+					os.Exit(1)
+				}
+				metaPath := filepath.Join(cwd, "meta.lua")
+				if err := processor.GenerateMetaFile(metaPath); err != nil {
+					mainLogger.Error("Failed to generate meta.lua: %v", err)
+					os.Exit(1)
+				}
+				return
+			}
+			if len(args) == 0 {
+				cmd.Usage()
+				return
+			}
+			runModifier(args, cmd)
+		},
+	}
+
+	// Global flags
+	rootCmd.PersistentFlags().StringP("loglevel", "l", "INFO", "Set logging level: ERROR, WARNING, INFO, DEBUG, TRACE")
+
+	// Local flags
+	rootCmd.Flags().IntP("parallel", "P", 100, "Number of files to process in parallel")
+	rootCmd.Flags().StringP("filter", "f", "", "Filter commands before running them")
+	rootCmd.Flags().Bool("json", false, "Enable JSON mode for processing JSON files")
+	rootCmd.Flags().BoolP("conv", "c", false, "Convert YAML files to TOML format")
+	rootCmd.Flags().BoolP("example", "e", false, "Generate example_cook.toml and exit")
+	rootCmd.Flags().BoolP("meta", "m", false, "Generate meta.lua file for LuaLS autocomplete and exit")
+
+	// Set up examples in the help text
+	rootCmd.SetUsageTemplate(`Usage:{{if .Runnable}}
+  {{.UseLine}}{{end}}{{if .HasAvailableSubCommands}}
+  {{.CommandPath}} [command]{{end}} {{if gt (len .Aliases) 0}}
+
+Aliases:
+  {{.NameAndAliases}}{{end}}{{if .HasExample}}
+
+Examples:
+{{.Example}}{{end}}{{if .HasAvailableSubCommands}}
+
+Available Commands:{{range .Commands}}{{if (or .IsAvailableCommand (eq .Name "help"))}}
+  {{rpad .Name .NamePadding }} {{.Short}}{{end}}{{end}}{{end}}{{if .HasAvailableLocalFlags}}
+
+Flags:
+{{.LocalFlags.FlagUsages | trimTrailingWhitespaces}}{{end}}{{if .HasAvailableInheritedFlags}}
+
+Global Flags:
+{{.InheritedFlags.FlagUsages | trimTrailingWhitespaces}}{{end}}{{if .HasHelpSubCommands}}
+
+Additional help topics:{{range .Commands}}{{if .IsAdditionalHelpTopicCommand}}
+  {{rpad .CommandPath .CommandPathPadding}} {{.Short}}{{end}}{{end}}{{end}}{{if .HasAvailableSubCommands}}
+
+Use "{{.CommandPath}} [command] --help" for more information about a command.{{end}}
+`)
+
+	// Add examples
+	rootCmd.Example = `  Regex mode (default):
+    modifier "<value>(\\d+)</value>" "*1.5" data.xml
+
+  JSON mode:
+    modifier -json data.json
+
+  YAML to TOML conversion:
+    modifier -conv *.yml
+    modifier -conv **/*.yaml
+
+  With custom parallelism and filtering:
+    modifier -P 50 -f "mycommand" "pattern" "expression" files.txt
+
+Note: v1, v2, etc. are used to refer to capture groups as numbers.
+      s1, s2, etc. are used to refer to capture groups as strings.
+      Helper functions: num(str) converts string to number, str(num) converts number to string
+      is_number(str) checks if a string is numeric
+      If expression starts with an operator like *, /, +, -, =, etc., v1 is automatically prepended
+      You can use any valid Lua code, including if statements, loops, etc.
+      Glob patterns are supported for file selection (*.xml, data/**.xml, etc.)
+
+` + processor.GetLuaFunctionsHelp()
+}
+
+func main() {
+	if err := rootCmd.Execute(); err != nil {
+		mainLogger.Error("Command execution failed: %v", err)
+		os.Exit(1)
+	}
+}
+
+func runModifier(args []string, cmd *cobra.Command) {
+	// Get flag values from Cobra
+	convertFlag, _ := cmd.Flags().GetBool("conv")
+	parallelFlag, _ := cmd.Flags().GetInt("parallel")
+	filterFlag, _ := cmd.Flags().GetString("filter")
+	jsonFlag, _ := cmd.Flags().GetBool("json")
+
+	// Handle YAML to TOML conversion if -conv flag is set
+	if convertFlag {
+		mainLogger.Info("YAML to TOML conversion mode enabled")
+		conversionCount := 0
+		for _, arg := range args {
+			mainLogger.Debug("Converting YAML files matching pattern: %s", arg)
+			err := utils.ConvertYAMLToTOML(arg)
+			if err != nil {
+				mainLogger.Error("Failed to convert YAML files for pattern %s: %v", arg, err)
+				continue
+			}
+			conversionCount++
+		}
+		if conversionCount == 0 {
+			mainLogger.Warning("No files were converted. Please check your patterns.")
+		} else {
+			mainLogger.Info("Conversion completed for %d pattern(s)", conversionCount)
+		}
+		return
+	}
+
+	mainLogger.Debug("Getting database connection")
+	db, err := utils.GetDB()
+	if err != nil {
+		mainLogger.Error("Failed to get database: %v", err)
+		return
+	}
+	mainLogger.Debug("Database connection established")
+
+	workdone, err := HandleSpecialArgs(args, db)
+	if err != nil {
+		mainLogger.Error("Failed to handle special args: %v", err)
+		return
+	}
+	if workdone {
+		mainLogger.Info("Special arguments handled, exiting.")
+		return
+	}
 
 	// The plan is:
 	// Load all commands
-	commands, err := utils.LoadCommands(args)
-	if err != nil {
-		logger.Error("Failed to load commands: %v", err)
-		flag.Usage()
+	mainLogger.Debug("Loading commands from arguments")
+	mainLogger.Trace("Arguments: %v", args)
+	commands, variables, err := utils.LoadCommands(args)
+	if err != nil || len(commands) == 0 {
+		mainLogger.Error("Failed to load commands: %v", err)
+		cmd.Usage()
 		return
 	}
+	if len(variables) > 0 {
+		mainLogger.Info("Loaded %d global variables", len(variables))
+		processor.SetVariables(variables)
+	}
+	mainLogger.Info("Loaded %d commands", len(commands))
+
+	if filterFlag != "" {
+		mainLogger.Info("Filtering commands by name: %s", filterFlag)
+		commands = utils.FilterCommands(commands, filterFlag)
+		mainLogger.Info("Filtered %d commands", len(commands))
+	}
 
 	// Then aggregate all the globs and deduplicate them
+	mainLogger.Debug("Aggregating globs and deduplicating")
 	globs := utils.AggregateGlobs(commands)
-	logger.Debug("Aggregated %d globs before deduplication", utils.CountGlobsBeforeDedup(commands))
+	mainLogger.Debug("Aggregated %d globs before deduplication", utils.CountGlobsBeforeDedup(commands))
+
+	for _, command := range commands {
+		mainLogger.Trace("Command: %s", command.Name)
+		if len(command.Regexes) > 0 {
+			mainLogger.Trace("Regexes: %v", command.Regexes)
+		} else {
+			mainLogger.Trace("Regex: %s", command.Regex)
+		}
+		mainLogger.Trace("Files: %v", command.Files)
+		mainLogger.Trace("Lua: %s", command.Lua)
+		mainLogger.Trace("Reset: %t", command.Reset)
+		mainLogger.Trace("Isolate: %t", command.Isolate)
+		mainLogger.Trace("LogLevel: %s", command.LogLevel)
+	}
 
 	// Resolve all the files for all the globs
-	logger.Info("Found %d unique file patterns", len(globs))
-	files, err := utils.ExpandGLobs(globs)
+	mainLogger.Info("Found %d unique file patterns", len(globs))
+	mainLogger.Debug("Expanding glob patterns to files")
+	files, err := utils.ExpandGlobs(globs)
 	if err != nil {
-		logger.Error("Failed to expand file patterns: %v", err)
+		mainLogger.Error("Failed to expand file patterns: %v", err)
 		return
 	}
-	logger.Info("Found %d files to process", len(files))
+	mainLogger.Info("Found %d files to process", len(files))
+	mainLogger.Trace("Files to process: %v", files)
 
 	// Somehow connect files to commands via globs..
 	// For each file check every glob of every command
 	// Maybe memoize this part
 	// That way we know what commands affect what files
+	mainLogger.Debug("Associating files with commands")
 	associations, err := utils.AssociateFilesWithCommands(files, commands)
 	if err != nil {
-		logger.Error("Failed to associate files with commands: %v", err)
+		mainLogger.Error("Failed to associate files with commands: %v", err)
 		return
 	}
+	mainLogger.Debug("Files associated with commands")
+	mainLogger.Trace("File-command associations: %v", associations)
+	// Per-file association summary for better visibility when debugging
+	for file, assoc := range associations {
+		cmdNames := make([]string, 0, len(assoc.Commands))
+		for _, c := range assoc.Commands {
+			cmdNames = append(cmdNames, c.Name)
+		}
+		isoNames := make([]string, 0, len(assoc.IsolateCommands))
+		for _, c := range assoc.IsolateCommands {
+			isoNames = append(isoNames, c.Name)
+		}
+		mainLogger.Debug("File %q has %d regular and %d isolate commands", file, len(assoc.Commands), len(assoc.IsolateCommands))
+		mainLogger.Trace("\tRegular: %v", cmdNames)
+		mainLogger.Trace("\tIsolate: %v", isoNames)
+	}
+
+	mainLogger.Debug("Resetting files where necessary")
+	err = utils.ResetWhereNecessary(associations, db)
+	if err != nil {
+		mainLogger.Error("Failed to reset files where necessary: %v", err)
+		return
+	}
+	mainLogger.Debug("Files reset where necessary")
 
-	// TODO: Utilize parallel workers for this
 	// Then for each file run all commands associated with the file
-	workers := make(chan struct{}, *utils.ParallelFiles)
+	workers := make(chan struct{}, parallelFlag)
 	wg := sync.WaitGroup{}
+	mainLogger.Debug("Starting file processing with %d parallel workers", parallelFlag)
 
 	// Add performance tracking
 	startTime := time.Now()
-	var fileMutex sync.Mutex
 
-	for file, commands := range associations {
+	// Create a map to store loggers for each command
+	commandLoggers := make(map[string]*logger.Logger)
+	for _, command := range commands {
+		// Create a named logger for each command
+		cmdName := command.Name
+		if cmdName == "" {
+			// If no name is provided, use a short version of the regex pattern
+			if len(command.Regex) > 20 {
+				cmdName = command.Regex[:17] + "..."
+			} else {
+				cmdName = command.Regex
+			}
+		}
+
+		// Parse the log level for this specific command
+		cmdLogLevel := logger.ParseLevel(command.LogLevel)
+
+		// Create a logger with the command name as a field
+		commandLoggers[command.Name] = logger.Default.WithField("command", cmdName)
+		commandLoggers[command.Name].SetLevel(cmdLogLevel)
+
+		mainLogger.Debug("Created logger for command %q with log level %s", cmdName, cmdLogLevel.String())
+	}
+
+	for file, association := range associations {
 		workers <- struct{}{}
 		wg.Add(1)
 		logger.SafeGoWithArgs(func(args ...interface{}) {
 			defer func() { <-workers }()
 			defer wg.Done()
-
 			// Track per-file processing time
 			fileStartTime := time.Now()
 
+			mainLogger.Debug("Reading file %q", file)
 			fileData, err := os.ReadFile(file)
 			if err != nil {
-				logger.Error("Failed to read file %q: %v", file, err)
+				mainLogger.Error("Failed to read file %q: %v", file, err)
+				atomic.AddInt64(&stats.FailedFiles, 1)
 				return
 			}
-			logger.Trace("Loaded %d bytes of data for file %q", len(fileData), file)
 			fileDataStr := string(fileData)
+			mainLogger.Trace("File %q content: %s", file, utils.LimitString(fileDataStr, 500))
 
-			// Aggregate all the modifications and execute them
-			modifications := []utils.ReplaceCommand{}
-			for _, command := range commands {
-				logger.Info("Processing file %q with command %q", file, command.Regex)
-				commands, err := processor.ProcessRegex(fileDataStr, command)
+			isChanged := false
+			mainLogger.Debug("Running isolate commands for file %q", file)
+			fileDataStr, err = RunIsolateCommands(association, file, fileDataStr, jsonFlag)
+			if err != nil && err != ErrNothingToDo {
+				mainLogger.Error("Failed to run isolate commands for file %q: %v", file, err)
+				atomic.AddInt64(&stats.FailedFiles, 1)
+				return
+			}
+			if err != ErrNothingToDo {
+				isChanged = true
+			}
+
+			mainLogger.Debug("Running other commands for file %q", file)
+			fileDataStr, err = RunOtherCommands(file, fileDataStr, association, commandLoggers, jsonFlag)
+			if err != nil && err != ErrNothingToDo {
+				mainLogger.Error("Failed to run other commands for file %q: %v", file, err)
+				atomic.AddInt64(&stats.FailedFiles, 1)
+				return
+			}
+			if err != ErrNothingToDo {
+				isChanged = true
+			}
+
+			if isChanged {
+				mainLogger.Debug("Saving file %q to database", file)
+				err = db.SaveFile(file, fileData)
 				if err != nil {
-					logger.Error("Failed to process file %q with command %q: %v", file, command.Regex, err)
+					mainLogger.Error("Failed to save file %q to database: %v", file, err)
+					atomic.AddInt64(&stats.FailedFiles, 1)
 					return
 				}
-				modifications = append(modifications, commands...)
-				// It is not guranteed that all the commands will be executed...
-				// TODO: Make this better
-				// We'd have to pass the map to executemodifications or something...
-				stats.ModificationsPerCommand[command.Name] += len(commands)
+				mainLogger.Debug("File %q saved to database", file)
 			}
 
-			if len(modifications) == 0 {
-				logger.Info("No modifications found for file %q", file)
-				return
-			}
-
-			// Sort commands in reverse order for safe replacements
-			fileDataStr, count := utils.ExecuteModifications(modifications, fileDataStr)
-
-			fileMutex.Lock()
-			stats.ProcessedFiles++
-			stats.TotalModifications += count
-			fileMutex.Unlock()
-
-			logger.Info("Executed %d modifications for file %q", count, file)
-
+			mainLogger.Debug("Writing file %q", file)
 			err = os.WriteFile(file, []byte(fileDataStr), 0644)
 			if err != nil {
-				logger.Error("Failed to write file %q: %v", file, err)
+				mainLogger.Error("Failed to write file %q: %v", file, err)
+				atomic.AddInt64(&stats.FailedFiles, 1)
 				return
 			}
+			mainLogger.Debug("File %q written", file)
 
-			logger.Debug("File %q processed in %v", file, time.Since(fileStartTime))
+			// Only increment ProcessedFiles once per file, after all processing is complete
+			atomic.AddInt64(&stats.ProcessedFiles, 1)
+
+			mainLogger.Debug("File %q processed in %v", file, time.Since(fileStartTime))
 		}, file, commands)
 	}
 	wg.Wait()
 
 	processingTime := time.Since(startTime)
-	logger.Info("Processing completed in %v", processingTime)
-	if stats.ProcessedFiles > 0 {
-		logger.Info("Average time per file: %v", processingTime/time.Duration(stats.ProcessedFiles))
+	mainLogger.Info("Processing completed in %v", processingTime)
+	processedFiles := atomic.LoadInt64(&stats.ProcessedFiles)
+	if processedFiles > 0 {
+		mainLogger.Info("Average time per file: %v", processingTime/time.Duration(processedFiles))
 	}
 
 	// TODO: Also give each command its own logger, maybe prefix it with something... Maybe give commands a name?
 	// Do that with logger.WithField("loglevel", level.String())
 	// Since each command also has its own log level
 	// TODO: Maybe even figure out how to run individual commands...?
-	// TODO: What to do with git? Figure it out ....
-
-	// if *gitFlag {
-	// 	logger.Info("Git integration enabled, setting up git repository")
-	// 	err := setupGit()
-	// 	if err != nil {
-	// 		logger.Error("Failed to setup git: %v", err)
-	// 		fmt.Fprintf(os.Stderr, "Error setting up git: %v\n", err)
-	// 		return
-	// 	}
-	// }
-
-	// logger.Debug("Expanding file patterns")
-	// files, err := expandFilePatterns(filePatterns)
-	// if err != nil {
-	// 	logger.Error("Failed to expand file patterns: %v", err)
-	// 	fmt.Fprintf(os.Stderr, "Error expanding file patterns: %v\n", err)
-	// 	return
-	// }
-
-	// if *gitFlag {
-	// 	logger.Info("Cleaning up git files before processing")
-	// 	err := cleanupGitFiles(files)
-	// 	if err != nil {
-	// 		logger.Error("Failed to cleanup git files: %v", err)
-	// 		fmt.Fprintf(os.Stderr, "Error cleaning up git files: %v\n", err)
-	// 		return
-	// 	}
-	// }
-	// if *resetFlag {
-	// 	logger.Info("Files reset to their original state, nothing more to do")
-	// 	log.Printf("Files reset to their original state, nothing more to do")
-	// 	return
-	// }
 
 	// Print summary
-	if stats.TotalModifications == 0 {
-		logger.Warning("No modifications were made in any files")
-		fmt.Fprintf(os.Stderr, "No modifications were made in any files\n")
+	totalModifications := atomic.LoadInt64(&stats.TotalModifications)
+	if totalModifications == 0 {
+		mainLogger.Warning("No modifications were made in any files")
 	} else {
-		logger.Info("Operation complete! Modified %d values in %d/%d files",
-			stats.TotalModifications, stats.ProcessedFiles, stats.ProcessedFiles+stats.FailedFiles)
-		fmt.Printf("Operation complete! Modified %d values in %d/%d files\n",
-			stats.TotalModifications, stats.ProcessedFiles, stats.ProcessedFiles+stats.FailedFiles)
+		failedFiles := atomic.LoadInt64(&stats.FailedFiles)
+		mainLogger.Info("Operation complete! Modified %d values in %d/%d files",
+			totalModifications, processedFiles, processedFiles+failedFiles)
+		sortedCommands := []string{}
+		stats.ModificationsPerCommand.Range(func(key, value interface{}) bool {
+			sortedCommands = append(sortedCommands, key.(string))
+			return true
+		})
+		sort.Strings(sortedCommands)
+
+		for _, command := range sortedCommands {
+			count, _ := stats.ModificationsPerCommand.Load(command)
+			if count.(int) > 0 {
+				mainLogger.Info("\tCommand %q made %d modifications", command, count)
+			} else {
+				mainLogger.Warning("\tCommand %q made no modifications", command)
+			}
+		}
 	}
 }
+
+func HandleSpecialArgs(args []string, db utils.DB) (bool, error) {
+	handleSpecialArgsLogger := logger.Default.WithPrefix("HandleSpecialArgs")
+	handleSpecialArgsLogger.Debug("Handling special arguments: %v", args)
+	if len(args) == 0 {
+		handleSpecialArgsLogger.Warning("No arguments provided to HandleSpecialArgs")
+		return false, nil
+	}
+	switch args[0] {
+	case "reset":
+		handleSpecialArgsLogger.Info("Resetting all files to their original state from database")
+		err := utils.ResetAllFiles(db)
+		if err != nil {
+			handleSpecialArgsLogger.Error("Failed to reset all files: %v", err)
+			return true, err
+		}
+		handleSpecialArgsLogger.Info("Successfully reset all files to original state")
+		return true, nil
+	case "dump":
+		handleSpecialArgsLogger.Info("Dumping all files from database (clearing snapshots)")
+		err := db.RemoveAllFiles()
+		if err != nil {
+			handleSpecialArgsLogger.Error("Failed to remove all files from database: %v", err)
+			return true, err
+		}
+		handleSpecialArgsLogger.Info("Successfully cleared all file snapshots from database")
+		return true, nil
+	default:
+		handleSpecialArgsLogger.Debug("Unknown special argument: %q", args[0])
+	}
+	handleSpecialArgsLogger.Debug("No special arguments handled, returning false")
+	return false, nil
+}
+
+func CreateExampleConfig() {
+	createExampleConfigLogger := logger.Default.WithPrefix("CreateExampleConfig")
+	createExampleConfigLogger.Debug("Creating example configuration file")
+
+	// Save the embedded TOML content to disk
+	createExampleConfigLogger.Debug("Writing example_cook.toml")
+	err := os.WriteFile("example_cook.toml", []byte(exampleTOMLContent), 0644)
+	if err != nil {
+		createExampleConfigLogger.Error("Failed to write example_cook.toml: %v", err)
+		return
+	}
+
+	createExampleConfigLogger.Info("Wrote example_cook.toml")
+}
+
+var ErrNothingToDo = errors.New("nothing to do")
+
+func RunOtherCommands(file string, fileDataStr string, association utils.FileCommandAssociation, commandLoggers map[string]*logger.Logger, jsonFlag bool) (string, error) {
+	runOtherCommandsLogger := mainLogger.WithPrefix("RunOtherCommands").WithField("file", file)
+	runOtherCommandsLogger.Debug("Running other commands for file")
+	runOtherCommandsLogger.Trace("File data before modifications: %s", utils.LimitString(fileDataStr, 200))
+
+	// Separate JSON and regex commands for different processing approaches
+	jsonCommands := []utils.ModifyCommand{}
+	regexCommands := []utils.ModifyCommand{}
+
+	for _, command := range association.Commands {
+		if command.JSON || jsonFlag {
+			jsonCommands = append(jsonCommands, command)
+		} else {
+			regexCommands = append(regexCommands, command)
+		}
+	}
+
+	// Process JSON commands sequentially (each operates on the entire file)
+	for _, command := range jsonCommands {
+		cmdLogger := logger.Default
+		if cmdLog, ok := commandLoggers[command.Name]; ok {
+			cmdLogger = cmdLog
+		}
+
+		cmdLogger.Debug("Processing file with JSON mode for command %q", command.Name)
+		newModifications, err := processor.ProcessJSON(fileDataStr, command, file)
+		if err != nil {
+			runOtherCommandsLogger.Error("Failed to process file with JSON command %q: %v", command.Name, err)
+			continue
+		}
+
+		// Apply JSON modifications immediately
+		if len(newModifications) > 0 {
+			var count int
+			fileDataStr, count = utils.ExecuteModifications(newModifications, fileDataStr)
+			atomic.AddInt64(&stats.TotalModifications, int64(count))
+			cmdLogger.Debug("Applied %d JSON modifications for command %q", count, command.Name)
+		}
+
+		count, ok := stats.ModificationsPerCommand.Load(command.Name)
+		if !ok {
+			count = 0
+		}
+		stats.ModificationsPerCommand.Store(command.Name, count.(int)+len(newModifications))
+	}
+
+	// Aggregate regex modifications and execute them
+	modifications := []utils.ReplaceCommand{}
+	numCommandsConsidered := 0
+	for _, command := range regexCommands {
+		cmdLogger := logger.Default
+		if cmdLog, ok := commandLoggers[command.Name]; ok {
+			cmdLogger = cmdLog
+		}
+
+		patterns := command.Regexes
+		if len(patterns) == 0 {
+			patterns = []string{command.Regex}
+		}
+		for idx, pattern := range patterns {
+			tmpCmd := command
+			tmpCmd.Regex = pattern
+			cmdLogger.Debug("Begin processing file with command %q (pattern %d/%d)", command.Name, idx+1, len(patterns))
+			numCommandsConsidered++
+			newModifications, err := processor.ProcessRegex(fileDataStr, tmpCmd, file)
+			if err != nil {
+				runOtherCommandsLogger.Error("Failed to process file with command %q: %v", command.Name, err)
+				continue
+			}
+			modifications = append(modifications, newModifications...)
+			count, ok := stats.ModificationsPerCommand.Load(command.Name)
+			if !ok {
+				count = 0
+			}
+			stats.ModificationsPerCommand.Store(command.Name, count.(int)+len(newModifications))
+
+			cmdLogger.Debug("Command %q generated %d modifications (pattern %d/%d)", command.Name, len(newModifications), idx+1, len(patterns))
+			cmdLogger.Trace("Modifications generated by command %q: %v", command.Name, newModifications)
+			if len(newModifications) == 0 {
+				cmdLogger.Debug("No modifications yielded by command %q (pattern %d/%d)", command.Name, idx+1, len(patterns))
+			}
+		}
+	}
+
+	runOtherCommandsLogger.Debug("Aggregated %d modifications from %d command-pattern runs", len(modifications), numCommandsConsidered)
+	runOtherCommandsLogger.Trace("All aggregated modifications: %v", modifications)
+
+	if len(modifications) == 0 {
+		runOtherCommandsLogger.Warning("No modifications found for file")
+		return fileDataStr, ErrNothingToDo
+	}
+	runOtherCommandsLogger.Debug("Executing %d modifications for file", len(modifications))
+
+	// Sort commands in reverse order for safe replacements
+	var count int
+	fileDataStr, count = utils.ExecuteModifications(modifications, fileDataStr)
+	runOtherCommandsLogger.Trace("File data after modifications: %s", utils.LimitString(fileDataStr, 200))
+
+	atomic.AddInt64(&stats.TotalModifications, int64(count))
+
+	runOtherCommandsLogger.Info("Executed %d modifications for file", count)
+	return fileDataStr, nil
+}
+
+func RunIsolateCommands(association utils.FileCommandAssociation, file string, fileDataStr string, jsonFlag bool) (string, error) {
+	runIsolateCommandsLogger := mainLogger.WithPrefix("RunIsolateCommands").WithField("file", file)
+	runIsolateCommandsLogger.Debug("Running isolate commands for file")
+	runIsolateCommandsLogger.Trace("File data before isolate modifications: %s", utils.LimitString(fileDataStr, 200))
+
+	anythingDone := false
+	currentFileData := fileDataStr
+
+	for _, isolateCommand := range association.IsolateCommands {
+		// Check if this isolate command should use JSON mode
+		if isolateCommand.JSON || jsonFlag {
+			runIsolateCommandsLogger.Debug("Begin processing file with JSON isolate command %q", isolateCommand.Name)
+			modifications, err := processor.ProcessJSON(currentFileData, isolateCommand, file)
+			if err != nil {
+				runIsolateCommandsLogger.Error("Failed to process file with JSON isolate command %q: %v", isolateCommand.Name, err)
+				continue
+			}
+
+			if len(modifications) == 0 {
+				runIsolateCommandsLogger.Debug("JSON isolate command %q produced no modifications", isolateCommand.Name)
+				continue
+			}
+			anythingDone = true
+
+			runIsolateCommandsLogger.Debug("Executing %d JSON isolate modifications for file", len(modifications))
+			runIsolateCommandsLogger.Trace("JSON isolate modifications: %v", modifications)
+			var count int
+			currentFileData, count = utils.ExecuteModifications(modifications, currentFileData)
+			runIsolateCommandsLogger.Trace("File data after JSON isolate modifications: %s", utils.LimitString(currentFileData, 200))
+
+			atomic.AddInt64(&stats.TotalModifications, int64(count))
+
+			cmdCount, ok := stats.ModificationsPerCommand.Load(isolateCommand.Name)
+			if !ok {
+				stats.ModificationsPerCommand.Store(isolateCommand.Name, 0)
+				cmdCount = 0
+			}
+			stats.ModificationsPerCommand.Store(isolateCommand.Name, cmdCount.(int)+len(modifications))
+
+			runIsolateCommandsLogger.Info("Executed %d JSON isolate modifications for file", count)
+		} else {
+			// Regular regex processing for isolate commands
+			patterns := isolateCommand.Regexes
+			if len(patterns) == 0 {
+				patterns = []string{isolateCommand.Regex}
+			}
+			for idx, pattern := range patterns {
+				tmpCmd := isolateCommand
+				tmpCmd.Regex = pattern
+				runIsolateCommandsLogger.Debug("Begin processing file with isolate command %q (pattern %d/%d)", isolateCommand.Name, idx+1, len(patterns))
+				modifications, err := processor.ProcessRegex(currentFileData, tmpCmd, file)
+				if err != nil {
+					runIsolateCommandsLogger.Error("Failed to process file with isolate command %q (pattern %d/%d): %v", isolateCommand.Name, idx+1, len(patterns), err)
+					continue
+				}
+
+				if len(modifications) == 0 {
+					runIsolateCommandsLogger.Debug("Isolate command %q produced no modifications (pattern %d/%d)", isolateCommand.Name, idx+1, len(patterns))
+					continue
+				}
+				anythingDone = true
+
+				runIsolateCommandsLogger.Debug("Executing %d isolate modifications for file", len(modifications))
+				runIsolateCommandsLogger.Trace("Isolate modifications: %v", modifications)
+				var count int
+				currentFileData, count = utils.ExecuteModifications(modifications, currentFileData)
+				runIsolateCommandsLogger.Trace("File data after isolate modifications: %s", utils.LimitString(currentFileData, 200))
+
+				atomic.AddInt64(&stats.TotalModifications, int64(count))
+
+				cmdCount, ok := stats.ModificationsPerCommand.Load(isolateCommand.Name)
+				if !ok {
+					stats.ModificationsPerCommand.Store(isolateCommand.Name, 0)
+					cmdCount = 0
+				}
+				stats.ModificationsPerCommand.Store(isolateCommand.Name, cmdCount.(int)+len(modifications))
+
+				runIsolateCommandsLogger.Info("Executed %d isolate modifications for file", count)
+			}
+		}
+	}
+	if !anythingDone {
+		runIsolateCommandsLogger.Debug("No isolate modifications were made for file")
+		return fileDataStr, ErrNothingToDo
+	}
+	return currentFileData, nil
+}

processor/json.go

@@ -0,0 +1,591 @@
+// Package processor provides JSON processing and Lua script execution capabilities
+// for data transformation and manipulation.
+package processor
+
+import (
+	"cook/utils"
+	"encoding/json"
+	"fmt"
+	"sort"
+	"strconv"
+	"strings"
+	"time"
+
+	logger "git.site.quack-lab.dev/dave/cylogger"
+	"github.com/tidwall/gjson"
+	lua "github.com/yuin/gopher-lua"
+)
+
+// jsonLogger is a scoped logger for the processor/json package.
+var jsonLogger = logger.Default.WithPrefix("processor/json")
+
+// ProcessJSON applies Lua processing to JSON content
+func ProcessJSON(content string, command utils.ModifyCommand, filename string) ([]utils.ReplaceCommand, error) {
+	processJSONLogger := jsonLogger.WithPrefix("ProcessJSON").WithField("commandName", command.Name).WithField("file", filename)
+	processJSONLogger.Debug("Starting JSON processing for file")
+	processJSONLogger.Trace("Initial file content length: %d", len(content))
+
+	var commands []utils.ReplaceCommand
+	startTime := time.Now()
+
+	// Parse JSON content
+	var jsonData interface{}
+	err := json.Unmarshal([]byte(content), &jsonData)
+	if err != nil {
+		processJSONLogger.Error("Failed to parse JSON content: %v", err)
+		return commands, fmt.Errorf("failed to parse JSON: %v", err)
+	}
+	processJSONLogger.Debug("Successfully parsed JSON content")
+
+	// Create Lua state
+	L, err := NewLuaState()
+	if err != nil {
+		processJSONLogger.Error("Error creating Lua state: %v", err)
+		return commands, fmt.Errorf("error creating Lua state: %v", err)
+	}
+	defer L.Close()
+
+	// Set filename global
+	L.SetGlobal("file", lua.LString(filename))
+
+	// Convert JSON data to Lua table
+	luaTable, err := ToLuaTable(L, jsonData)
+	if err != nil {
+		processJSONLogger.Error("Failed to convert JSON to Lua table: %v", err)
+		return commands, fmt.Errorf("failed to convert JSON to Lua table: %v", err)
+	}
+
+	// Set the JSON data as a global variable
+	L.SetGlobal("data", luaTable)
+	processJSONLogger.Debug("Set JSON data as Lua global 'data'")
+
+	// Build and execute Lua script for JSON mode
+	luaExpr := BuildJSONLuaScript(command.Lua, command.SourceDir)
+	processJSONLogger.Debug("Built Lua script from expression: %q", command.Lua)
+	processJSONLogger.Trace("Full Lua script: %q", utils.LimitString(luaExpr, 200))
+
+	if err := L.DoString(luaExpr); err != nil {
+		processJSONLogger.Error("Lua script execution failed: %v\nScript: %s", err, utils.LimitString(luaExpr, 200))
+		return commands, fmt.Errorf("lua script execution failed: %v", err)
+	}
+	processJSONLogger.Debug("Lua script executed successfully")
+
+	// Check if modification flag is set
+	modifiedVal := L.GetGlobal("modified")
+	if modifiedVal.Type() != lua.LTBool || !lua.LVAsBool(modifiedVal) {
+		processJSONLogger.Debug("Skipping - no modifications indicated by Lua script")
+		return commands, nil
+	}
+
+	// Get the modified data from Lua
+	modifiedData := L.GetGlobal("data")
+	if modifiedData.Type() != lua.LTTable {
+		processJSONLogger.Error("Expected 'data' to be a table after Lua processing, got %s", modifiedData.Type().String())
+		return commands, fmt.Errorf("expected 'data' to be a table after Lua processing")
+	}
+
+	// Convert back to Go interface
+	goData, err := FromLua(L, modifiedData)
+	if err != nil {
+		processJSONLogger.Error("Failed to convert Lua table back to Go: %v", err)
+		return commands, fmt.Errorf("failed to convert Lua table back to Go: %v", err)
+	}
+
+	processJSONLogger.Debug("About to call applyChanges with original data and modified data")
+	commands, err = applyChanges(content, jsonData, goData)
+	if err != nil {
+		processJSONLogger.Error("Failed to apply surgical JSON changes: %v", err)
+		return commands, fmt.Errorf("failed to apply surgical JSON changes: %v", err)
+	}
+
+	processJSONLogger.Debug("Total JSON processing time: %v", time.Since(startTime))
+	processJSONLogger.Debug("Generated %d total modifications", len(commands))
+	return commands, nil
+}
+
+// applyChanges attempts to make surgical changes while preserving exact formatting
+func applyChanges(content string, originalData, modifiedData interface{}) ([]utils.ReplaceCommand, error) {
+	var commands []utils.ReplaceCommand
+
+	// Find all changes between original and modified data
+	changes := findDeepChanges("", originalData, modifiedData)
+
+	jsonLogger.Debug("applyChanges: Found %d changes: %v", len(changes), changes)
+
+	if len(changes) == 0 {
+		return commands, nil
+	}
+
+	// Sort removal operations by index in descending order to avoid index shifting
+	var removals []string
+	var additions []string
+	var valueChanges []string
+
+	for path := range changes {
+		if strings.HasSuffix(path, "@remove") {
+			removals = append(removals, path)
+		} else if strings.HasSuffix(path, "@add") {
+			additions = append(additions, path)
+		} else {
+			valueChanges = append(valueChanges, path)
+		}
+	}
+
+	jsonLogger.Debug("applyChanges: %d removals, %d additions, %d value changes", len(removals), len(additions), len(valueChanges))
+
+	// Apply removals first (from end to beginning to avoid index shifting)
+	for _, removalPath := range removals {
+		actualPath := strings.TrimSuffix(removalPath, "@remove")
+		elementIndex := extractIndexFromRemovalPath(actualPath)
+		arrayPath := getArrayPathFromElementPath(actualPath)
+
+		jsonLogger.Debug("Processing removal: path=%s, index=%d, arrayPath=%s", actualPath, elementIndex, arrayPath)
+
+		// Find the exact byte range to remove
+		from, to := findArrayElementRemovalRange(content, arrayPath, elementIndex)
+
+		jsonLogger.Debug("Removing bytes %d-%d", from, to)
+
+		commands = append(commands, utils.ReplaceCommand{
+			From: from,
+			To:   to,
+			With: "",
+		})
+
+		jsonLogger.Debug("Added removal command: From=%d, To=%d, With=\"\"", from, to)
+	}
+
+	// Apply additions (new fields)
+	for _, additionPath := range additions {
+		actualPath := strings.TrimSuffix(additionPath, "@add")
+		newValue := changes[additionPath]
+
+		jsonLogger.Debug("Processing addition: path=%s, value=%v", actualPath, newValue)
+
+		// Find the parent object to add the field to
+		parentPath := getParentPath(actualPath)
+		fieldName := getFieldName(actualPath)
+
+		jsonLogger.Debug("Parent path: %s, field name: %s", parentPath, fieldName)
+
+		// Get the parent object
+		var parentResult gjson.Result
+		if parentPath == "" {
+			// Adding to root object - get the entire JSON
+			parentResult = gjson.Parse(content)
+		} else {
+			parentResult = gjson.Get(content, parentPath)
+		}
+
+		if !parentResult.Exists() {
+			jsonLogger.Debug("Parent path %s does not exist, skipping", parentPath)
+			continue
+		}
+
+		// Find where to insert the new field (at the end of the object)
+		startPos := int(parentResult.Index + len(parentResult.Raw) - 1) // Before closing brace
+
+		jsonLogger.Debug("Inserting at pos %d", startPos)
+
+		// Convert the new value to JSON string
+		newValueStr := convertValueToJSONString(newValue)
+
+		// Insert the new field with pretty-printed formatting
+		// Format: ,"fieldName": { ... }
+		insertText := fmt.Sprintf(`,"%s": %s`, fieldName, newValueStr)
+
+		commands = append(commands, utils.ReplaceCommand{
+			From: startPos,
+			To:   startPos,
+			With: insertText,
+		})
+
+		jsonLogger.Debug("Added addition command: From=%d, To=%d, With=%q", startPos, startPos, insertText)
+	}
+
+	// Apply value changes (in reverse order to avoid position shifting)
+	sort.Slice(valueChanges, func(i, j int) bool {
+		// Get positions for comparison
+		resultI := gjson.Get(content, valueChanges[i])
+		resultJ := gjson.Get(content, valueChanges[j])
+		return resultI.Index > resultJ.Index // Descending order
+	})
+
+	for _, path := range valueChanges {
+		newValue := changes[path]
+
+		jsonLogger.Debug("Processing value change: path=%s, value=%v", path, newValue)
+
+		// Get the current value and its position in the original JSON
+		result := gjson.Get(content, path)
+		if !result.Exists() {
+			jsonLogger.Debug("Path %s does not exist, skipping", path)
+			continue // Skip if path doesn't exist
+		}
+
+		// Get the exact byte positions of this value
+		startPos := result.Index
+		endPos := startPos + len(result.Raw)
+
+		jsonLogger.Debug("Found value at pos %d-%d: %q", startPos, endPos, result.Raw)
+
+		// Convert the new value to JSON string
+		newValueStr := convertValueToJSONString(newValue)
+
+		jsonLogger.Debug("Converting to: %q", newValueStr)
+
+		// Create a replacement command for this specific value
+		commands = append(commands, utils.ReplaceCommand{
+			From: int(startPos),
+			To:   int(endPos),
+			With: newValueStr,
+		})
+
+		jsonLogger.Debug("Added command: From=%d, To=%d, With=%q", int(startPos), int(endPos), newValueStr)
+	}
+
+	return commands, nil
+}
+
+// extractIndexFromRemovalPath extracts the array index from a removal path like "Rows.0.Inputs.1@remove"
+func extractIndexFromRemovalPath(path string) int {
+	parts := strings.Split(strings.TrimSuffix(path, "@remove"), ".")
+	if len(parts) > 0 {
+		lastPart := parts[len(parts)-1]
+		if index, err := strconv.Atoi(lastPart); err == nil {
+			return index
+		}
+	}
+	return -1
+}
+
+// getArrayPathFromElementPath converts "Rows.0.Inputs.1" to "Rows.0.Inputs"
+func getArrayPathFromElementPath(elementPath string) string {
+	parts := strings.Split(elementPath, ".")
+	if len(parts) > 0 {
+		return strings.Join(parts[:len(parts)-1], ".")
+	}
+	return ""
+}
+
+// getParentPath extracts the parent path from a full path like "Rows.0.Inputs.1"
+func getParentPath(fullPath string) string {
+	parts := strings.Split(fullPath, ".")
+	if len(parts) > 0 {
+		return strings.Join(parts[:len(parts)-1], ".")
+	}
+	return ""
+}
+
+// getFieldName extracts the field name from a full path like "Rows.0.Inputs.1"
+func getFieldName(fullPath string) string {
+	parts := strings.Split(fullPath, ".")
+	if len(parts) > 0 {
+		return parts[len(parts)-1]
+	}
+	return ""
+}
+
+// convertValueToJSONString converts a Go interface{} to a JSON string representation
+func convertValueToJSONString(value interface{}) string {
+	switch v := value.(type) {
+	case string:
+		return `"` + strings.ReplaceAll(v, `"`, `\"`) + `"`
+	case float64:
+		if v == float64(int64(v)) {
+			return strconv.FormatInt(int64(v), 10)
+		}
+		return strconv.FormatFloat(v, 'f', -1, 64)
+	case bool:
+		return strconv.FormatBool(v)
+	case nil:
+		return "null"
+	case map[string]interface{}:
+		// Handle maps specially to avoid double-escaping of keys
+		var pairs []string
+		for key, val := range v {
+			// The key might already have escaped quotes from Lua, so we need to be careful
+			// If the key already contains escaped quotes, we need to unescape them first
+			keyStr := key
+			if strings.Contains(key, `\"`) {
+				// Key already has escaped quotes, use it as-is
+				keyStr = `"` + key + `"`
+			} else {
+				// Normal key, escape quotes
+				keyStr = `"` + strings.ReplaceAll(key, `"`, `\"`) + `"`
+			}
+			valStr := convertValueToJSONString(val)
+			pairs = append(pairs, keyStr+":"+valStr)
+		}
+		return "{" + strings.Join(pairs, ",") + "}"
+	default:
+		// For other complex types (arrays), we need to use json.Marshal
+		jsonBytes, err := json.Marshal(v)
+		if err != nil {
+			return "null" // Fallback to null if marshaling fails
+		}
+		return string(jsonBytes)
+	}
+}
+
+// findArrayElementRemovalRange finds the exact byte range to remove for an array element
+func findArrayElementRemovalRange(content, arrayPath string, elementIndex int) (int, int) {
+	// Get the array using gjson
+	var arrayResult gjson.Result
+	if arrayPath == "" {
+		// Root-level array
+		arrayResult = gjson.Parse(content)
+	} else {
+		arrayResult = gjson.Get(content, arrayPath)
+	}
+
+	if !arrayResult.Exists() || !arrayResult.IsArray() {
+		return -1, -1
+	}
+
+	// Get all array elements
+	elements := arrayResult.Array()
+	if elementIndex >= len(elements) {
+		return -1, -1
+	}
+
+	// Get the target element
+	elementResult := elements[elementIndex]
+	startPos := int(elementResult.Index)
+	endPos := int(elementResult.Index + len(elementResult.Raw))
+
+	// Handle comma removal properly
+	if elementIndex == 0 && len(elements) > 1 {
+		// First element but not the only one - remove comma after
+		for i := endPos; i < len(content) && i < endPos+50; i++ {
+			if content[i] == ',' {
+				endPos = i + 1
+				break
+			}
+		}
+	} else if elementIndex == len(elements)-1 && len(elements) > 1 {
+		// Last element and not the only one - remove comma before
+		prevElementEnd := int(elements[elementIndex-1].Index + len(elements[elementIndex-1].Raw))
+		for i := prevElementEnd; i < startPos && i < len(content); i++ {
+			if content[i] == ',' {
+				startPos = i
+				break
+			}
+		}
+	}
+	// If it's the only element, don't remove any commas
+
+	return startPos, endPos
+}
+
+// findDeepChanges recursively finds all paths that need to be changed
+func findDeepChanges(basePath string, original, modified interface{}) map[string]interface{} {
+	changes := make(map[string]interface{})
+
+	switch orig := original.(type) {
+	case map[string]interface{}:
+		if mod, ok := modified.(map[string]interface{}); ok {
+			// Check for new keys added in modified data
+			for key, modValue := range mod {
+				var currentPath string
+				if basePath == "" {
+					currentPath = key
+				} else {
+					currentPath = basePath + "." + key
+				}
+
+				if origValue, exists := orig[key]; exists {
+					// Key exists in both, check if value changed
+					switch modValue.(type) {
+					case map[string]interface{}, []interface{}:
+						// Recursively check nested structures
+						nestedChanges := findDeepChanges(currentPath, origValue, modValue)
+						for nestedPath, nestedValue := range nestedChanges {
+							changes[nestedPath] = nestedValue
+						}
+					default:
+						// Primitive value - check if changed
+						if !deepEqual(origValue, modValue) {
+							changes[currentPath] = modValue
+						}
+					}
+				} else {
+					// New key added - mark for addition
+					changes[currentPath+"@add"] = modValue
+				}
+			}
+		}
+	case []interface{}:
+		if mod, ok := modified.([]interface{}); ok {
+			// Handle array changes by detecting specific element operations
+			if len(orig) != len(mod) {
+				// Array length changed - detect if it's element removal
+				if len(orig) > len(mod) {
+					// Element(s) removed - find which ones by comparing content
+					removedIndices := findRemovedArrayElements(orig, mod)
+					for _, removedIndex := range removedIndices {
+						var currentPath string
+						if basePath == "" {
+							currentPath = fmt.Sprintf("%d@remove", removedIndex)
+						} else {
+							currentPath = fmt.Sprintf("%s.%d@remove", basePath, removedIndex)
+						}
+						changes[currentPath] = nil // Mark for removal
+					}
+				}
+			} else {
+				// Same length - check individual elements for value changes
+				for i, modValue := range mod {
+					var currentPath string
+					if basePath == "" {
+						currentPath = strconv.Itoa(i)
+					} else {
+						currentPath = basePath + "." + strconv.Itoa(i)
+					}
+
+					if i < len(orig) {
+						// Index exists in both, check if value changed
+						switch modValue.(type) {
+						case map[string]interface{}, []interface{}:
+							// Recursively check nested structures
+							nestedChanges := findDeepChanges(currentPath, orig[i], modValue)
+							for nestedPath, nestedValue := range nestedChanges {
+								changes[nestedPath] = nestedValue
+							}
+						default:
+							// Primitive value - check if changed
+							if !deepEqual(orig[i], modValue) {
+								changes[currentPath] = modValue
+							}
+						}
+					}
+				}
+			}
+		}
+	}
+	// Note: No default case needed - JSON data from unmarshaling is always
+	// map[string]interface{} or []interface{} at the top level
+
+	return changes
+}
+
+// findRemovedArrayElements compares two arrays and returns indices of removed elements
+func findRemovedArrayElements(original, modified []interface{}) []int {
+	var removedIndices []int
+
+	// Simple approach: find elements in original that don't exist in modified
+	for i, origElement := range original {
+		found := false
+		for _, modElement := range modified {
+			if deepEqual(origElement, modElement) {
+				found = true
+				break
+			}
+		}
+		if !found {
+			removedIndices = append(removedIndices, i)
+		}
+	}
+
+	return removedIndices
+}
+
+// deepEqual performs deep comparison of two values
+func deepEqual(a, b interface{}) bool {
+	if a == nil && b == nil {
+		return true
+	}
+	if a == nil || b == nil {
+		return false
+	}
+
+	switch av := a.(type) {
+	case map[string]interface{}:
+		if bv, ok := b.(map[string]interface{}); ok {
+			if len(av) != len(bv) {
+				return false
+			}
+			for k, v := range av {
+				if !deepEqual(v, bv[k]) {
+					return false
+				}
+			}
+			return true
+		}
+		return false
+	case []interface{}:
+		if bv, ok := b.([]interface{}); ok {
+			if len(av) != len(bv) {
+				return false
+			}
+			for i, v := range av {
+				if !deepEqual(v, bv[i]) {
+					return false
+				}
+			}
+			return true
+		}
+		return false
+	default:
+		return a == b
+	}
+}
+
+// ToLuaTable converts a Go interface{} (map or array) to a Lua table
+// This should only be called with map[string]interface{} or []interface{} from JSON unmarshaling
+func ToLuaTable(L *lua.LState, data interface{}) (*lua.LTable, error) {
+	switch v := data.(type) {
+	case map[string]interface{}:
+		table := L.CreateTable(0, len(v))
+		for key, value := range v {
+			table.RawSetString(key, ToLuaValue(L, value))
+		}
+		return table, nil
+
+	case []interface{}:
+		table := L.CreateTable(len(v), 0)
+		for i, value := range v {
+			table.RawSetInt(i+1, ToLuaValue(L, value)) // Lua arrays are 1-indexed
+		}
+		return table, nil
+
+	default:
+		// This should only happen with invalid JSON (root-level primitives)
+		return nil, fmt.Errorf("expected table or array, got %T", v)
+	}
+}
+
+// ToLuaValue converts a Go interface{} to a Lua value
+func ToLuaValue(L *lua.LState, data interface{}) lua.LValue {
+	switch v := data.(type) {
+	case map[string]interface{}:
+		table := L.CreateTable(0, len(v))
+		for key, value := range v {
+			table.RawSetString(key, ToLuaValue(L, value))
+		}
+		return table
+
+	case []interface{}:
+		table := L.CreateTable(len(v), 0)
+		for i, value := range v {
+			table.RawSetInt(i+1, ToLuaValue(L, value)) // Lua arrays are 1-indexed
+		}
+		return table
+
+	case string:
+		return lua.LString(v)
+
+	case float64:
+		return lua.LNumber(v)
+
+	case bool:
+		return lua.LBool(v)
+
+	case nil:
+		return lua.LNil
+
+	default:
+		// This should never happen with JSON-unmarshaled data
+		return lua.LNil
+	}
+}

processor/json_coverage_test.go

@@ -0,0 +1,283 @@
+package processor
+
+import (
+	"cook/utils"
+	"testing"
+
+	"github.com/stretchr/testify/assert"
+)
+
+// TestJSONFloat tests line 298 - float formatting for non-integer floats
+func TestJSONFloatFormatting(t *testing.T) {
+	jsonContent := `{
+  "value": 10.5,
+  "another": 3.14159
+}`
+
+	command := utils.ModifyCommand{
+		Name: "test_float",
+		JSON: true,
+		Lua: `
+data.value = data.value * 2
+data.another = data.another * 10
+modified = true
+`,
+	}
+
+	commands, err := ProcessJSON(jsonContent, command, "test.json")
+	assert.NoError(t, err)
+	assert.NotEmpty(t, commands)
+
+	result, _ := utils.ExecuteModifications(commands, jsonContent)
+	assert.Contains(t, result, "21")      // 10.5 * 2
+	assert.Contains(t, result, "31.4159") // 3.14159 * 10
+}
+
+// TestJSONNestedObjectAddition tests lines 303-320 - map[string]interface{} case
+func TestJSONNestedObjectAddition(t *testing.T) {
+	jsonContent := `{
+  "items": {}
+}`
+
+	command := utils.ModifyCommand{
+		Name: "test_nested",
+		JSON: true,
+		Lua: `
+data.items.newObject = {
+	name = "test",
+	value = 42,
+	enabled = true
+}
+modified = true
+`,
+	}
+
+	commands, err := ProcessJSON(jsonContent, command, "test.json")
+	assert.NoError(t, err)
+	assert.NotEmpty(t, commands)
+
+	result, _ := utils.ExecuteModifications(commands, jsonContent)
+	assert.Contains(t, result, `"newObject"`)
+	assert.Contains(t, result, `"name"`)
+	assert.Contains(t, result, `"test"`)
+	assert.Contains(t, result, `"value"`)
+	assert.Contains(t, result, "42")
+}
+
+// TestJSONKeyWithQuotes tests line 315 - key escaping with quotes
+func TestJSONKeyWithQuotes(t *testing.T) {
+	jsonContent := `{
+  "data": {}
+}`
+
+	command := utils.ModifyCommand{
+		Name: "test_key_quotes",
+		JSON: true,
+		Lua: `
+data.data["key-with-dash"] = "value1"
+data.data.normalKey = "value2"
+modified = true
+`,
+	}
+
+	commands, err := ProcessJSON(jsonContent, command, "test.json")
+	assert.NoError(t, err)
+	assert.NotEmpty(t, commands)
+
+	result, _ := utils.ExecuteModifications(commands, jsonContent)
+	assert.Contains(t, result, `"key-with-dash"`)
+	assert.Contains(t, result, `"normalKey"`)
+}
+
+// TestJSONArrayInValue tests lines 321-327 - default case with json.Marshal for arrays
+func TestJSONArrayInValue(t *testing.T) {
+	jsonContent := `{
+  "data": {}
+}`
+
+	command := utils.ModifyCommand{
+		Name: "test_array_value",
+		JSON: true,
+		Lua: `
+data.data.items = {1, 2, 3, 4, 5}
+data.data.strings = {"a", "b", "c"}
+modified = true
+`,
+	}
+
+	commands, err := ProcessJSON(jsonContent, command, "test.json")
+	assert.NoError(t, err)
+	assert.NotEmpty(t, commands)
+
+	result, _ := utils.ExecuteModifications(commands, jsonContent)
+	assert.Contains(t, result, `"items"`)
+	assert.Contains(t, result, `[1,2,3,4,5]`)
+	assert.Contains(t, result, `"strings"`)
+	assert.Contains(t, result, `["a","b","c"]`)
+}
+
+// TestJSONRootArrayElementRemoval tests line 422 - removing from root-level array
+func TestJSONRootArrayElementRemoval(t *testing.T) {
+	jsonContent := `[
+  {"id": 1, "name": "first"},
+  {"id": 2, "name": "second"},
+  {"id": 3, "name": "third"}
+]`
+
+	command := utils.ModifyCommand{
+		Name: "test_root_array_removal",
+		JSON: true,
+		Lua: `
+-- Remove the second element
+table.remove(data, 2)
+modified = true
+`,
+	}
+
+	commands, err := ProcessJSON(jsonContent, command, "test.json")
+	assert.NoError(t, err)
+	assert.NotEmpty(t, commands)
+
+	result, _ := utils.ExecuteModifications(commands, jsonContent)
+	assert.Contains(t, result, `"first"`)
+	assert.Contains(t, result, `"third"`)
+	assert.NotContains(t, result, `"second"`)
+}
+
+// TestJSONRootArrayElementChange tests lines 434 and 450 - changing primitive values in root array
+func TestJSONRootArrayElementChange(t *testing.T) {
+	jsonContent := `[10, 20, 30, 40, 50]`
+
+	command := utils.ModifyCommand{
+		Name: "test_root_array_change",
+		JSON: true,
+		Lua: `
+-- Double all values
+for i = 1, #data do
+	data[i] = data[i] * 2
+end
+modified = true
+`,
+	}
+
+	commands, err := ProcessJSON(jsonContent, command, "test.json")
+	assert.NoError(t, err)
+	assert.NotEmpty(t, commands)
+
+	result, _ := utils.ExecuteModifications(commands, jsonContent)
+	assert.Contains(t, result, "20")
+	assert.Contains(t, result, "40")
+	assert.Contains(t, result, "60")
+	assert.Contains(t, result, "80")
+	assert.Contains(t, result, "100")
+	assert.NotContains(t, result, "10,")
+}
+
+// TestJSONRootArrayStringElements tests deepEqual with strings in root array
+func TestJSONRootArrayStringElements(t *testing.T) {
+	jsonContent := `["apple", "banana", "cherry"]`
+
+	command := utils.ModifyCommand{
+		Name: "test_root_array_strings",
+		JSON: true,
+		Lua: `
+data[2] = "orange"
+modified = true
+`,
+	}
+
+	commands, err := ProcessJSON(jsonContent, command, "test.json")
+	assert.NoError(t, err)
+	assert.NotEmpty(t, commands)
+
+	result, _ := utils.ExecuteModifications(commands, jsonContent)
+	assert.Contains(t, result, `"apple"`)
+	assert.Contains(t, result, `"orange"`)
+	assert.Contains(t, result, `"cherry"`)
+	assert.NotContains(t, result, `"banana"`)
+}
+
+// TestJSONComplexNestedStructure tests multiple untested paths together
+func TestJSONComplexNestedStructure(t *testing.T) {
+	jsonContent := `{
+  "config": {
+    "multiplier": 2.5
+  }
+}`
+
+	command := utils.ModifyCommand{
+		Name: "test_complex",
+		JSON: true,
+		Lua: `
+-- Add nested object with array
+data.config.settings = {
+	enabled = true,
+	values = {1.5, 2.5, 3.5},
+	names = {"alpha", "beta"}
+}
+-- Change float
+data.config.multiplier = 7.777
+modified = true
+`,
+	}
+
+	commands, err := ProcessJSON(jsonContent, command, "test.json")
+	assert.NoError(t, err)
+	assert.NotEmpty(t, commands)
+
+	result, _ := utils.ExecuteModifications(commands, jsonContent)
+	assert.Contains(t, result, "7.777")
+	assert.Contains(t, result, `"settings"`)
+	assert.Contains(t, result, `"values"`)
+	assert.Contains(t, result, `[1.5,2.5,3.5]`)
+}
+
+// TestJSONRemoveFirstArrayElement tests line 358-365 - removing first element with comma handling
+func TestJSONRemoveFirstArrayElement(t *testing.T) {
+	jsonContent := `{
+  "items": [1, 2, 3, 4, 5]
+}`
+
+	command := utils.ModifyCommand{
+		Name: "test_remove_first",
+		JSON: true,
+		Lua: `
+table.remove(data.items, 1)
+modified = true
+`,
+	}
+
+	commands, err := ProcessJSON(jsonContent, command, "test.json")
+	assert.NoError(t, err)
+	assert.NotEmpty(t, commands)
+
+	result, _ := utils.ExecuteModifications(commands, jsonContent)
+	assert.NotContains(t, result, "[1,")
+	assert.Contains(t, result, "2")
+	assert.Contains(t, result, "5")
+}
+
+// TestJSONRemoveLastArrayElement tests line 366-374 - removing last element with comma handling
+func TestJSONRemoveLastArrayElement(t *testing.T) {
+	jsonContent := `{
+  "items": [1, 2, 3, 4, 5]
+}`
+
+	command := utils.ModifyCommand{
+		Name: "test_remove_last",
+		JSON: true,
+		Lua: `
+table.remove(data.items, 5)
+modified = true
+`,
+	}
+
+	commands, err := ProcessJSON(jsonContent, command, "test.json")
+	assert.NoError(t, err)
+	assert.NotEmpty(t, commands)
+
+	result, _ := utils.ExecuteModifications(commands, jsonContent)
+	assert.Contains(t, result, "1")
+	assert.Contains(t, result, "4")
+	assert.NotContains(t, result, ", 5")
+}

processor/json_deepequal_test.go

@@ -0,0 +1,153 @@
+package processor
+
+import (
+	"testing"
+
+	"github.com/stretchr/testify/assert"
+)
+
+func TestDeepEqual(t *testing.T) {
+	tests := []struct {
+		name     string
+		a        interface{}
+		b        interface{}
+		expected bool
+	}{
+		{
+			name:     "both nil",
+			a:        nil,
+			b:        nil,
+			expected: true,
+		},
+		{
+			name:     "first nil",
+			a:        nil,
+			b:        "something",
+			expected: false,
+		},
+		{
+			name:     "second nil",
+			a:        "something",
+			b:        nil,
+			expected: false,
+		},
+		{
+			name:     "equal primitives",
+			a:        42,
+			b:        42,
+			expected: true,
+		},
+		{
+			name:     "different primitives",
+			a:        42,
+			b:        43,
+			expected: false,
+		},
+		{
+			name:     "equal strings",
+			a:        "hello",
+			b:        "hello",
+			expected: true,
+		},
+		{
+			name: "equal maps",
+			a: map[string]interface{}{
+				"key1": "value1",
+				"key2": 42,
+			},
+			b: map[string]interface{}{
+				"key1": "value1",
+				"key2": 42,
+			},
+			expected: true,
+		},
+		{
+			name: "maps different lengths",
+			a: map[string]interface{}{
+				"key1": "value1",
+			},
+			b: map[string]interface{}{
+				"key1": "value1",
+				"key2": 42,
+			},
+			expected: false,
+		},
+		{
+			name: "maps different values",
+			a: map[string]interface{}{
+				"key1": "value1",
+			},
+			b: map[string]interface{}{
+				"key1": "value2",
+			},
+			expected: false,
+		},
+		{
+			name: "map vs non-map",
+			a: map[string]interface{}{
+				"key1": "value1",
+			},
+			b:        "not a map",
+			expected: false,
+		},
+		{
+			name:     "equal arrays",
+			a:        []interface{}{1, 2, 3},
+			b:        []interface{}{1, 2, 3},
+			expected: true,
+		},
+		{
+			name:     "arrays different lengths",
+			a:        []interface{}{1, 2},
+			b:        []interface{}{1, 2, 3},
+			expected: false,
+		},
+		{
+			name:     "arrays different values",
+			a:        []interface{}{1, 2, 3},
+			b:        []interface{}{1, 2, 4},
+			expected: false,
+		},
+		{
+			name:     "array vs non-array",
+			a:        []interface{}{1, 2, 3},
+			b:        "not an array",
+			expected: false,
+		},
+		{
+			name: "nested equal structures",
+			a: map[string]interface{}{
+				"outer": map[string]interface{}{
+					"inner": []interface{}{1, 2, 3},
+				},
+			},
+			b: map[string]interface{}{
+				"outer": map[string]interface{}{
+					"inner": []interface{}{1, 2, 3},
+				},
+			},
+			expected: true,
+		},
+		{
+			name: "nested different structures",
+			a: map[string]interface{}{
+				"outer": map[string]interface{}{
+					"inner": []interface{}{1, 2, 3},
+				},
+			},
+			b: map[string]interface{}{
+				"outer": map[string]interface{}{
+					"inner": []interface{}{1, 2, 4},
+				},
+			},
+			expected: false,
+		},
+	}
+
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			result := deepEqual(tt.a, tt.b)
+			assert.Equal(t, tt.expected, result)
+		})
+	}
+}

processor/json_test.go

@@ -0,0 +1,95 @@
+package processor
+
+import (
+	"cook/utils"
+	"testing"
+
+	"github.com/stretchr/testify/assert"
+)
+
+func TestProcessJSON(t *testing.T) {
+	tests := []struct {
+		name           string
+		input          string
+		luaExpression  string
+		expectedOutput string
+		expectedMods   int
+	}{
+		{
+			name:           "Basic JSON object modification",
+			input:          `{"name": "test", "value": 42}`,
+			luaExpression:  `data.value = data.value * 2; return true`,
+			expectedOutput: `{"name": "test", "value": 84}`,
+			expectedMods:   1,
+		},
+		{
+			name:           "JSON array modification",
+			input:          `{"items": [{"name": "item1", "value": 10}, {"name": "item2", "value": 20}]}`,
+			luaExpression:  `for i, item in ipairs(data.items) do item.value = item.value * 2 end modified = true`,
+			expectedOutput: `{"items": [{"name": "item1", "value": 20}, {"name": "item2", "value": 40}]}`,
+			expectedMods:   2, 
+		},
+		{
+			name:           "JSON nested object modification",
+			input:          `{"config": {"setting1": {"enabled": true, "value": 5}, "setting2": {"enabled": false, "value": 10}}}`,
+			luaExpression:  `data.config.setting1.enabled = false data.config.setting2.value = 15 modified = true`,
+			expectedOutput: `{"config": {"setting1": {"enabled": false, "value": 5}, "setting2": {"enabled": false, "value": 15}}}`,
+			expectedMods:   2,
+		},
+		{
+			name:           "JSON no modification",
+			input:          `{"name": "test", "value": 42}`,
+			luaExpression:  `return false`,
+			expectedOutput: `{"name": "test", "value": 42}`,
+			expectedMods:   0,
+		},
+	}
+
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			command := utils.ModifyCommand{
+				Name: tt.name,
+				JSON: true,
+				Lua:  tt.luaExpression,
+			}
+
+			modifications, err := ProcessJSON(tt.input, command, "test.json")
+			assert.NoError(t, err, "ProcessJSON failed: %v", err)
+
+			if len(modifications) > 0 {
+				// Execute modifications
+				result, count := utils.ExecuteModifications(modifications, tt.input)
+				assert.Equal(t, tt.expectedMods, count, "Expected %d modifications, got %d", tt.expectedMods, count)
+				assert.Equal(t, tt.expectedOutput, result, "Expected output: %s, got: %s", tt.expectedOutput, result)
+			} else {
+				assert.Equal(t, 0, tt.expectedMods, "Expected no modifications but got some")
+			}
+		})
+	}
+}
+
+func TestToLuaValue(t *testing.T) {
+	L, err := NewLuaState()
+	if err != nil {
+		t.Fatalf("Failed to create Lua state: %v", err)
+	}
+	defer L.Close()
+
+	tests := []struct {
+		name     string
+		input    interface{}
+		expected string
+	}{
+		{"string", "hello", "hello"},
+		{"number", 42.0, "42"},
+		{"boolean", true, "true"},
+		{"nil", nil, "nil"},
+	}
+
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			result := ToLuaValue(L, tt.input)
+			assert.Equal(t, tt.expected, result.String())
+		})
+	}
+}

processor/lua_external_integration_test.go

@@ -0,0 +1,191 @@
+package processor
+
+import (
+	"os"
+	"path/filepath"
+	"testing"
+
+	"cook/utils"
+
+	"github.com/stretchr/testify/assert"
+)
+
+func TestProcessRegexWithExternalLuaFile(t *testing.T) {
+	tmpDir, err := os.MkdirTemp("", "lua-external-integration-test-*")
+	assert.NoError(t, err)
+	defer os.RemoveAll(tmpDir)
+
+	// Create a test Lua file with replacement variable
+	luaFile := filepath.Join(tmpDir, "multiply.lua")
+	luaContent := `v1 = v1 * 2
+replacement = format("<value>%s</value>", v1)
+return true`
+	err = os.WriteFile(luaFile, []byte(luaContent), 0644)
+	assert.NoError(t, err)
+
+	// Create test content
+	content := `<value>10</value>`
+
+	// Create command with external Lua reference
+	command := utils.ModifyCommand{
+		Name:      "test",
+		Regex:     `<value>(\d+)</value>`,
+		Lua:       "@" + filepath.Base(luaFile),
+		SourceDir: tmpDir,
+	}
+
+	// Process
+	modifications, err := ProcessRegex(content, command, "test.xml")
+	assert.NoError(t, err)
+	assert.Greater(t, len(modifications), 0)
+	
+	// Apply modifications
+	result := content
+	for _, mod := range modifications {
+		result = result[:mod.From] + mod.With + result[mod.To:]
+	}
+	assert.Contains(t, result, "<value>20</value>")
+}
+
+func TestProcessJSONWithExternalLuaFile(t *testing.T) {
+	tmpDir, err := os.MkdirTemp("", "lua-external-json-integration-test-*")
+	assert.NoError(t, err)
+	defer os.RemoveAll(tmpDir)
+
+	// Create a test Lua file
+	luaFile := filepath.Join(tmpDir, "json_modify.lua")
+	luaContent := `data.value = 84
+modified = true`
+	err = os.WriteFile(luaFile, []byte(luaContent), 0644)
+	assert.NoError(t, err)
+
+	// Create test JSON content
+	content := `{"value": 42}`
+
+	// Create command with external Lua reference
+	command := utils.ModifyCommand{
+		Name:      "test",
+		JSON:      true,
+		Lua:       "@" + filepath.Base(luaFile),
+		SourceDir: tmpDir,
+	}
+
+	// Process
+	modifications, err := ProcessJSON(content, command, "test.json")
+	assert.NoError(t, err)
+	assert.Greater(t, len(modifications), 0)
+
+	// Apply modifications to verify
+	result := content
+	for _, mod := range modifications {
+		result = result[:mod.From] + mod.With + result[mod.To:]
+	}
+	// Check that value was changed to 84 (formatting may vary)
+	assert.Contains(t, result, `"value"`)
+	assert.Contains(t, result, `84`)
+	assert.NotContains(t, result, `"value": 42`)
+	assert.NotContains(t, result, `"value":42`)
+}
+
+func TestProcessXMLWithExternalLuaFile(t *testing.T) {
+	tmpDir, err := os.MkdirTemp("", "lua-external-xml-integration-test-*")
+	assert.NoError(t, err)
+	defer os.RemoveAll(tmpDir)
+
+	// Create a test Lua file (XML uses 'root' not 'data')
+	luaFile := filepath.Join(tmpDir, "xml_modify.lua")
+	luaContent := `visitElements(root, function(elem)
+    if elem._tag == "Item" then
+        modifyNumAttr(elem, "Weight", function(val) return val * 2 end)
+    end
+end)
+modified = true`
+	err = os.WriteFile(luaFile, []byte(luaContent), 0644)
+	assert.NoError(t, err)
+
+	// Create test XML content
+	content := `<Items><Item Weight="10" /></Items>`
+
+	// Create command with external Lua reference
+	command := utils.ModifyCommand{
+		Name:      "test",
+		Lua:       "@" + filepath.Base(luaFile),
+		SourceDir: tmpDir,
+	}
+
+	// Process
+	modifications, err := ProcessXML(content, command, "test.xml")
+	assert.NoError(t, err)
+	assert.Greater(t, len(modifications), 0)
+
+	// Apply modifications to verify
+	result := content
+	for _, mod := range modifications {
+		result = result[:mod.From] + mod.With + result[mod.To:]
+	}
+	assert.Contains(t, result, `Weight="20"`)
+}
+
+func TestExternalLuaFileWithVariables(t *testing.T) {
+	tmpDir, err := os.MkdirTemp("", "lua-external-vars-integration-test-*")
+	assert.NoError(t, err)
+	defer os.RemoveAll(tmpDir)
+
+	// Create a test Lua file with variable reference
+	luaFile := filepath.Join(tmpDir, "with_vars.lua")
+	luaContent := `v1 = v1 * $multiply
+replacement = format("<value>%s</value>", v1)
+return true`
+	err = os.WriteFile(luaFile, []byte(luaContent), 0644)
+	assert.NoError(t, err)
+
+	// Set global variable
+	SetVariables(map[string]interface{}{"multiply": 1.5})
+	defer SetVariables(map[string]interface{}{})
+
+	// Create test content
+	content := `<value>10</value>`
+
+	// Create command with external Lua reference
+	command := utils.ModifyCommand{
+		Name:      "test",
+		Regex:     `<value>(\d+)</value>`,
+		Lua:       "@" + filepath.Base(luaFile),
+		SourceDir: tmpDir,
+	}
+
+	// Process
+	modifications, err := ProcessRegex(content, command, "test.xml")
+	assert.NoError(t, err)
+	assert.Greater(t, len(modifications), 0)
+	
+	// Apply modifications
+	result := content
+	for _, mod := range modifications {
+		result = result[:mod.From] + mod.With + result[mod.To:]
+	}
+	assert.Contains(t, result, "<value>15</value>")
+}
+
+func TestExternalLuaFileErrorHandling(t *testing.T) {
+	tmpDir, err := os.MkdirTemp("", "lua-external-error-test-*")
+	assert.NoError(t, err)
+	defer os.RemoveAll(tmpDir)
+
+	// Create command with non-existent external Lua file
+	command := utils.ModifyCommand{
+		Name:      "test",
+		Regex:     `<value>(\d+)</value>`,
+		Lua:       "@nonexistent.lua",
+		SourceDir: tmpDir,
+	}
+
+	// Process - the error script will be generated but execution will fail
+	// ProcessRegex continues on Lua errors, so no modifications will be made
+	content := `<value>10</value>`
+	modifications, err := ProcessRegex(content, command, "test.xml")
+	
+	// No error returned (ProcessRegex continues on Lua errors), but no modifications made
+	assert.NoError(t, err)
+	assert.Empty(t, modifications)
+}

processor/lua_external_test.go

@@ -0,0 +1,224 @@
+package processor
+
+import (
+	"os"
+	"path/filepath"
+	"testing"
+
+	"github.com/stretchr/testify/assert"
+)
+
+func TestLoadExternalLuaFile(t *testing.T) {
+	tmpDir, err := os.MkdirTemp("", "lua-external-test-*")
+	assert.NoError(t, err)
+	defer os.RemoveAll(tmpDir)
+
+	// Create a test Lua file
+	luaFile := filepath.Join(tmpDir, "test.lua")
+	luaContent := `data.value = 42
+modified = true`
+	err = os.WriteFile(luaFile, []byte(luaContent), 0644)
+	assert.NoError(t, err)
+
+	tests := []struct {
+		name      string
+		luaPath   string
+		sourceDir string
+		expected  string
+		wantError bool
+	}{
+		{
+			name:      "Relative path with sourceDir",
+			luaPath:   "test.lua",
+			sourceDir: tmpDir,
+			expected:  luaContent,
+			wantError: false,
+		},
+		{
+			name:      "Absolute path",
+			luaPath:   luaFile,
+			sourceDir: "",
+			expected:  luaContent,
+			wantError: false,
+		},
+		{
+			name:      "Relative path without sourceDir (uses CWD)",
+			luaPath:   filepath.Base(luaFile),
+			sourceDir: "",
+			expected:  luaContent,
+			wantError: false,
+		},
+		{
+			name:      "Nested relative path",
+			luaPath:   "scripts/test.lua",
+			sourceDir: tmpDir,
+			expected:  "",
+			wantError: true,
+		},
+		{
+			name:      "Non-existent file",
+			luaPath:   "nonexistent.lua",
+			sourceDir: tmpDir,
+			expected:  "",
+			wantError: true,
+		},
+	}
+
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			// Change to tmpDir for CWD-based tests
+			if tt.sourceDir == "" && !filepath.IsAbs(tt.luaPath) {
+				origDir, _ := os.Getwd()
+				defer os.Chdir(origDir)
+				os.Chdir(tmpDir)
+			}
+
+			result, err := LoadExternalLuaFile(tt.luaPath, tt.sourceDir)
+			if tt.wantError {
+				assert.Error(t, err)
+				assert.Empty(t, result)
+			} else {
+				assert.NoError(t, err)
+				assert.Equal(t, tt.expected, result)
+			}
+		})
+	}
+}
+
+func TestBuildLuaScriptWithExternalFile(t *testing.T) {
+	tmpDir, err := os.MkdirTemp("", "lua-external-build-test-*")
+	assert.NoError(t, err)
+	defer os.RemoveAll(tmpDir)
+
+	// Create a test Lua file
+	luaFile := filepath.Join(tmpDir, "multiply.lua")
+	luaContent := `v1 = v1 * 2`
+	err = os.WriteFile(luaFile, []byte(luaContent), 0644)
+	assert.NoError(t, err)
+
+	// Test with relative path
+	relativePath := filepath.Base(luaFile)
+	result := BuildLuaScript("@"+relativePath, tmpDir)
+	assert.Contains(t, result, "v1 = v1 * 2")
+	assert.Contains(t, result, "function run()")
+
+	// Test with absolute path
+	result = BuildLuaScript("@"+luaFile, "")
+	assert.Contains(t, result, "v1 = v1 * 2")
+}
+
+func TestBuildLuaScriptWithExternalFileError(t *testing.T) {
+	// Test that missing file returns error script
+	result := BuildLuaScript("@nonexistent.lua", "/tmp")
+	assert.Contains(t, result, "error(")
+	assert.Contains(t, result, "Failed to load external Lua file")
+}
+
+func TestBuildJSONLuaScriptWithExternalFile(t *testing.T) {
+	tmpDir, err := os.MkdirTemp("", "lua-external-json-test-*")
+	assert.NoError(t, err)
+	defer os.RemoveAll(tmpDir)
+
+	// Create a test Lua file
+	luaFile := filepath.Join(tmpDir, "json_modify.lua")
+	luaContent := `data.value = 84
+modified = true`
+	err = os.WriteFile(luaFile, []byte(luaContent), 0644)
+	assert.NoError(t, err)
+
+	// Test with relative path
+	relativePath := filepath.Base(luaFile)
+	result := BuildJSONLuaScript("@"+relativePath, tmpDir)
+	assert.Contains(t, result, "data.value = 84")
+	assert.Contains(t, result, "modified = true")
+	assert.Contains(t, result, "function run()")
+}
+
+func TestBuildLuaScriptWithInlineCode(t *testing.T) {
+	// Test that inline code (without @) still works
+	result := BuildLuaScript("v1 = v1 * 2", "")
+	assert.Contains(t, result, "v1 = v1 * 2")
+	assert.Contains(t, result, "function run()")
+	assert.NotContains(t, result, "@")
+}
+
+func TestBuildLuaScriptExternalFileWithVariables(t *testing.T) {
+	tmpDir, err := os.MkdirTemp("", "lua-external-vars-test-*")
+	assert.NoError(t, err)
+	defer os.RemoveAll(tmpDir)
+
+	// Create a test Lua file with variable reference
+	luaFile := filepath.Join(tmpDir, "with_vars.lua")
+	luaContent := `v1 = v1 * $multiply`
+	err = os.WriteFile(luaFile, []byte(luaContent), 0644)
+	assert.NoError(t, err)
+
+	// Set a global variable
+	SetVariables(map[string]interface{}{"multiply": 1.5})
+	defer SetVariables(map[string]interface{}{})
+
+	// Test that variables are substituted in external files
+	result := BuildLuaScript("@"+filepath.Base(luaFile), tmpDir)
+	assert.Contains(t, result, "v1 = v1 * 1.5")
+	assert.NotContains(t, result, "$multiply")
+}
+
+func TestBuildLuaScriptExternalFileNestedPath(t *testing.T) {
+	tmpDir, err := os.MkdirTemp("", "lua-external-nested-test-*")
+	assert.NoError(t, err)
+	defer os.RemoveAll(tmpDir)
+
+	// Create nested directory structure
+	scriptsDir := filepath.Join(tmpDir, "scripts")
+	err = os.MkdirAll(scriptsDir, 0755)
+	assert.NoError(t, err)
+
+	luaFile := filepath.Join(scriptsDir, "test.lua")
+	luaContent := `data.value = 100`
+	err = os.WriteFile(luaFile, []byte(luaContent), 0644)
+	assert.NoError(t, err)
+
+	// Test with nested relative path
+	result := BuildLuaScript("@scripts/test.lua", tmpDir)
+	assert.Contains(t, result, "data.value = 100")
+}
+
+func TestBuildLuaScriptExternalFileWithPrependLuaAssignment(t *testing.T) {
+	tmpDir, err := os.MkdirTemp("", "lua-external-prepend-test-*")
+	assert.NoError(t, err)
+	defer os.RemoveAll(tmpDir)
+
+	// Create a test Lua file with operator prefix (should trigger prepend)
+	luaFile := filepath.Join(tmpDir, "multiply.lua")
+	luaContent := `* 2`
+	err = os.WriteFile(luaFile, []byte(luaContent), 0644)
+	assert.NoError(t, err)
+
+	// Test that prepend still works with external files
+	result := BuildLuaScript("@"+filepath.Base(luaFile), tmpDir)
+	// PrependLuaAssignment adds "v1 = v1" + "* 2" = "v1 = v1* 2" (no space between v1 and *)
+	assert.Contains(t, result, "v1 = v1* 2")
+}
+
+func TestBuildLuaScriptExternalFilePreservesWhitespace(t *testing.T) {
+	tmpDir, err := os.MkdirTemp("", "lua-external-whitespace-test-*")
+	assert.NoError(t, err)
+	defer os.RemoveAll(tmpDir)
+
+	// Create a test Lua file with multiline content
+	luaFile := filepath.Join(tmpDir, "multiline.lua")
+	luaContent := `if data.items then
+    for i, item in ipairs(data.items) do
+        item.value = item.value * 2
+    end
+    modified = true
+end`
+	err = os.WriteFile(luaFile, []byte(luaContent), 0644)
+	assert.NoError(t, err)
+
+	// Test that whitespace and formatting is preserved
+	result := BuildLuaScript("@"+filepath.Base(luaFile), tmpDir)
+	assert.Contains(t, result, "if data.items then")
+	assert.Contains(t, result, "    for i, item in ipairs(data.items) do")
+	assert.Contains(t, result, "        item.value = item.value * 2")
+}

processor/luahelper-test-regress.lua

@@ -0,0 +1,43 @@
+-- Load the helper script
+dofile("luahelper.lua")
+
+-- Test helper function
+local function assert(condition, message)
+	if not condition then error("ASSERTION FAILED: " .. (message or "unknown error")) end
+end
+
+local function test(name, fn)
+	local ok, err = pcall(fn)
+	if ok then
+		print("PASS: " .. name)
+	else
+		print("FAIL: " .. name .. " - " .. tostring(err))
+	end
+end
+
+test("regression test 001", function()
+	local csv =
+		[[Id	Enabled	ModuleId	DepartmentId	IsDepartment	PositionInGraph	Parents	Modifiers	UpgradePrice
+news_department	TRUE	navigation		TRUE	2 0		NewsAnalyticsDepartment + 1	communication_relay communication_relay
+nd_charge_bonus	TRUE	navigation	news_department	FALSE	1 0	news_department	NDSkillChargeBonus + 1	expert_disk expert_disk
+nd_cooldown_time_reduce	TRUE	navigation	news_department	FALSE	3 0	news_department	NDCooldownTimeReduce - 2	communication_relay communication_relay]]
+	local rows, err = fromCSV(csv, { delimiter = "\t", hasheader = true, hascomments = true })
+	if err then error("fromCSV error: " .. err) end
+	assert(#rows == 3, "Should have 3 rows")
+	assert(rows[1].Id == "news_department", "First row Id should be 'news_department'")
+	assert(rows[1].Enabled == "TRUE", "First row Enabled should be 'TRUE'")
+	assert(rows[1].ModuleId == "navigation", "First row ModuleId should be 'navigation'")
+	assert(rows[1].DepartmentId == "", "First row DepartmentId should be ''")
+	assert(rows[1].IsDepartment == "TRUE", "First row IsDepartment should be 'TRUE'")
+	assert(rows.Headers[1] == "Id", "First row Headers should be 'Id'")
+	assert(rows.Headers[2] == "Enabled", "First row Headers should be 'Enabled'")
+	assert(rows.Headers[3] == "ModuleId", "First row Headers should be 'ModuleId'")
+	assert(rows.Headers[4] == "DepartmentId", "First row Headers should be 'DepartmentId'")
+	assert(rows.Headers[5] == "IsDepartment", "First row Headers should be 'IsDepartment'")
+	assert(rows.Headers[6] == "PositionInGraph", "First row Headers should be 'PositionInGraph'")
+	assert(rows.Headers[7] == "Parents", "First row Headers should be 'Parents'")
+	assert(rows.Headers[8] == "Modifiers", "First row Headers should be 'Modifiers'")
+	assert(rows.Headers[9] == "UpgradePrice", "First row Headers should be 'UpgradePrice'")
+end)
+
+print("\nAll tests completed!")

processor/luahelper-test-xml.lua

@@ -0,0 +1,224 @@
+-- Load the helper script
+dofile("luahelper.lua")
+
+-- Test helper function
+local function assert(condition, message)
+	if not condition then error("ASSERTION FAILED: " .. (message or "unknown error")) end
+end
+
+local function test(name, fn)
+	local ok, err = pcall(fn)
+	if ok then
+		print("PASS: " .. name)
+	else
+		print("FAIL: " .. name .. " - " .. tostring(err))
+	end
+end
+
+-- Test findElements
+test("findElements finds all matching elements recursively", function()
+	local testXML = {
+		_tag = "root",
+		_children = {
+			{ _tag = "item", _attr = { name = "sword" } },
+			{ _tag = "item", _attr = { name = "shield" } },
+			{
+				_tag = "container",
+				_children = {
+					{ _tag = "item", _attr = { name = "potion" } },
+				},
+			},
+		},
+	}
+	local items = findElements(testXML, "item")
+	assert(#items == 3, "Should find 3 items total (recursive)")
+	assert(items[1]._attr.name == "sword", "First item should be sword")
+	assert(items[3]._attr.name == "potion", "Third item should be potion (from nested)")
+end)
+
+-- Test getNumAttr and setNumAttr
+test("getNumAttr gets numeric attribute", function()
+	local elem = { _tag = "item", _attr = { damage = "10" } }
+	local damage = getNumAttr(elem, "damage")
+	assert(damage == 10, "Should get damage as number")
+end)
+
+test("getNumAttr returns nil for missing attribute", function()
+	local elem = { _tag = "item", _attr = {} }
+	local damage = getNumAttr(elem, "damage")
+	assert(damage == nil, "Should return nil for missing attribute")
+end)
+
+test("setNumAttr sets numeric attribute", function()
+	local elem = { _tag = "item", _attr = {} }
+	setNumAttr(elem, "damage", 20)
+	assert(elem._attr.damage == "20", "Should set damage as string")
+end)
+
+-- Test modifyNumAttr
+test("modifyNumAttr modifies numeric attribute", function()
+	local elem = { _tag = "item", _attr = { weight = "5.5" } }
+	local modified = modifyNumAttr(elem, "weight", function(val) return val * 2 end)
+	assert(modified == true, "Should return true when modified")
+	assert(elem._attr.weight == "11.0", "Should double weight")
+end)
+
+test("modifyNumAttr returns false for missing attribute", function()
+	local elem = { _tag = "item", _attr = {} }
+	local modified = modifyNumAttr(elem, "weight", function(val) return val * 2 end)
+	assert(modified == false, "Should return false when attribute missing")
+end)
+
+-- Test filterElements
+test("filterElements filters by predicate", function()
+	local testXML = {
+		_tag = "root",
+		_children = {
+			{ _tag = "item", _attr = { healing = "20" } },
+			{ _tag = "item", _attr = { damage = "10" } },
+			{ _tag = "item", _attr = { healing = "50" } },
+		},
+	}
+	local healingItems = filterElements(testXML, function(elem) return hasAttr(elem, "healing") end)
+	assert(#healingItems == 2, "Should find 2 healing items")
+end)
+
+-- Test visitElements
+test("visitElements visits all elements", function()
+	local testXML = {
+		_tag = "root",
+		_children = {
+			{ _tag = "item" },
+			{ _tag = "container", _children = {
+				{ _tag = "item" },
+			} },
+		},
+	}
+	local count = 0
+	visitElements(testXML, function(elem) count = count + 1 end)
+	assert(count == 4, "Should visit 4 elements (root + 2 items + container)")
+end)
+
+-- Test getText and setText
+test("getText gets text content", function()
+	local elem = { _tag = "item", _text = "Iron Sword" }
+	local text = getText(elem)
+	assert(text == "Iron Sword", "Should get text content")
+end)
+
+test("setText sets text content", function()
+	local elem = { _tag = "item" }
+	setText(elem, "New Text")
+	assert(elem._text == "New Text", "Should set text content")
+end)
+
+-- Test hasAttr and getAttr
+test("hasAttr checks attribute existence", function()
+	local elem = { _tag = "item", _attr = { damage = "10" } }
+	assert(hasAttr(elem, "damage") == true, "Should have damage")
+	assert(hasAttr(elem, "magic") == false, "Should not have magic")
+end)
+
+test("getAttr gets attribute value", function()
+	local elem = { _tag = "item", _attr = { name = "sword" } }
+	assert(getAttr(elem, "name") == "sword", "Should get name attribute")
+	assert(getAttr(elem, "missing") == nil, "Should return nil for missing")
+end)
+
+test("setAttr sets attribute value", function()
+	local elem = { _tag = "item" }
+	setAttr(elem, "name", "sword")
+	assert(elem._attr.name == "sword", "Should set attribute")
+end)
+
+-- Test findFirstElement
+test("findFirstElement finds first direct child", function()
+	local parent = {
+		_tag = "root",
+		_children = {
+			{ _tag = "item", _attr = { id = "1" } },
+			{ _tag = "item", _attr = { id = "2" } },
+		},
+	}
+	local first = findFirstElement(parent, "item")
+	assert(first._attr.id == "1", "Should find first item")
+end)
+
+test("findFirstElement returns nil when not found", function()
+	local parent = { _tag = "root", _children = {} }
+	local result = findFirstElement(parent, "item")
+	assert(result == nil, "Should return nil when not found")
+end)
+
+-- Test getChildren
+test("getChildren gets all direct children with tag", function()
+	local parent = {
+		_tag = "root",
+		_children = {
+			{ _tag = "item", _attr = { id = "1" } },
+			{ _tag = "config" },
+			{ _tag = "item", _attr = { id = "2" } },
+		},
+	}
+	local items = getChildren(parent, "item")
+	assert(#items == 2, "Should get 2 items")
+	assert(items[1]._attr.id == "1", "First should have id=1")
+	assert(items[2]._attr.id == "2", "Second should have id=2")
+end)
+
+-- Test countChildren
+test("countChildren counts direct children with tag", function()
+	local parent = {
+		_tag = "root",
+		_children = {
+			{ _tag = "item" },
+			{ _tag = "config" },
+			{ _tag = "item" },
+		},
+	}
+	assert(countChildren(parent, "item") == 2, "Should count 2 items")
+	assert(countChildren(parent, "config") == 1, "Should count 1 config")
+end)
+
+-- Test addChild
+test("addChild adds child element", function()
+	local parent = { _tag = "root", _children = {} }
+	addChild(parent, { _tag = "item" })
+	assert(#parent._children == 1, "Should have 1 child")
+	assert(parent._children[1]._tag == "item", "Child should be item")
+end)
+
+test("addChild creates children array if needed", function()
+	local parent = { _tag = "root" }
+	addChild(parent, { _tag = "item" })
+	assert(parent._children ~= nil, "Should create _children")
+	assert(#parent._children == 1, "Should have 1 child")
+end)
+
+-- Test removeChildren
+test("removeChildren removes all matching children", function()
+	local parent = {
+		_tag = "root",
+		_children = {
+			{ _tag = "item" },
+			{ _tag = "config" },
+			{ _tag = "item" },
+		},
+	}
+	local removed = removeChildren(parent, "item")
+	assert(removed == 2, "Should remove 2 items")
+	assert(#parent._children == 1, "Should have 1 child left")
+	assert(parent._children[1]._tag == "config", "Remaining should be config")
+end)
+
+test("removeChildren returns 0 when none found", function()
+	local parent = {
+		_tag = "root",
+		_children = { { _tag = "item" } },
+	}
+	local removed = removeChildren(parent, "config")
+	assert(removed == 0, "Should remove 0")
+	assert(#parent._children == 1, "Should still have 1 child")
+end)
+
+print("\nAll tests completed!")

processor/luahelper-test.lua

@@ -0,0 +1,534 @@
+-- Load the helper script
+dofile("luahelper.lua")
+
+-- Test helper function
+local function assert(condition, message)
+	if not condition then error("ASSERTION FAILED: " .. (message or "unknown error")) end
+end
+
+local function test(name, fn)
+	local ok, err = pcall(fn)
+	if ok then
+		print("PASS: " .. name)
+	else
+		print("FAIL: " .. name .. " - " .. tostring(err))
+	end
+end
+
+-- Test fromCSV option validation
+test("fromCSV invalid option", function()
+	local csv = "a,b,c\n1,2,3"
+	local ok, errMsg = pcall(function() fromCSV(csv, { invalidOption = true }) end)
+	assert(ok == false, "Should raise error")
+	assert(string.find(errMsg, "unknown option"), "Error should mention unknown option")
+end)
+
+-- Test toCSV invalid delimiter
+test("toCSV invalid delimiter", function()
+	local rows = { { "a", "b", "c" } }
+	local csv = toCSV(rows, { delimiter = 123 })
+	-- toCSV converts delimiter to string, so 123 becomes "123"
+	assert(csv == "a123b123c", "Should convert delimiter to string")
+end)
+
+-- Test fromCSV basic parsing
+test("fromCSV basic", function()
+	local csv = "a,b,c\n1,2,3\n4,5,6"
+	local rows = fromCSV(csv)
+	assert(#rows == 3, "Should have 3 rows")
+	assert(rows[1][1] == "a", "First row first field should be 'a'")
+	assert(rows[2][2] == "2", "Second row second field should be '2'")
+end)
+
+-- Test fromCSV with headers
+test("fromCSV with headers", function()
+	local csv = "foo,bar,baz\n1,2,3\n4,5,6"
+	local rows = fromCSV(csv, { hasheader = true })
+	assert(#rows == 2, "Should have 2 data rows")
+	assert(rows[1][1] == "1", "First row first field should be '1'")
+	assert(rows[1].foo == "1", "First row foo should be '1'")
+	assert(rows[1].bar == "2", "First row bar should be '2'")
+	assert(rows[1].baz == "3", "First row baz should be '3'")
+end)
+
+-- Test fromCSV with custom delimiter
+test("fromCSV with tab delimiter", function()
+	local csv = "a\tb\tc\n1\t2\t3"
+	local rows = fromCSV(csv, { delimiter = "\t" })
+	assert(#rows == 2, "Should have 2 rows")
+	assert(rows[1][1] == "a", "First row first field should be 'a'")
+	assert(rows[2][2] == "2", "Second row second field should be '2'")
+end)
+
+-- Test fromCSV with quoted fields
+test("fromCSV with quoted fields", function()
+	local csv = '"hello,world","test"\n"foo","bar"'
+	local rows = fromCSV(csv)
+	assert(#rows == 2, "Should have 2 rows")
+	assert(rows[1][1] == "hello,world", "Quoted field with comma should be preserved")
+	assert(rows[1][2] == "test", "Second field should be 'test'")
+end)
+
+-- Test toCSV basic
+test("toCSV basic", function()
+	local rows = { { "a", "b", "c" }, { "1", "2", "3" } }
+	local csv = toCSV(rows)
+	assert(csv == "a,b,c\n1,2,3", "CSV output should match expected")
+end)
+
+-- Test toCSV with custom delimiter
+test("toCSV with tab delimiter", function()
+	local rows = { { "a", "b", "c" }, { "1", "2", "3" } }
+	local csv = toCSV(rows, { delimiter = "\t" })
+	assert(csv == "a\tb\tc\n1\t2\t3", "TSV output should match expected")
+end)
+
+-- Test toCSV with fields needing quoting
+test("toCSV with quoted fields", function()
+	local rows = { { "hello,world", "test" }, { "foo", "bar" } }
+	local csv = toCSV(rows)
+	assert(csv == '"hello,world",test\nfoo,bar', "Fields with commas should be quoted")
+end)
+
+-- Test round trip
+test("fromCSV toCSV round trip", function()
+	local original = "a,b,c\n1,2,3\n4,5,6"
+	local rows = fromCSV(original)
+	local csv = toCSV(rows)
+	assert(csv == original, "Round trip should preserve original")
+end)
+
+-- Test round trip with headers
+test("fromCSV toCSV round trip with headers", function()
+	local original = "foo,bar,baz\n1,2,3\n4,5,6"
+	local rows = fromCSV(original, { hasheader = true })
+	local csv = toCSV(rows)
+	local expected = "1,2,3\n4,5,6"
+	assert(csv == expected, "Round trip with headers should preserve data rows")
+end)
+
+-- Test fromCSV with comments
+test("fromCSV with comments", function()
+	local csv = "# This is a comment\nfoo,bar,baz\n1,2,3\n# Another comment\n4,5,6"
+	local rows = fromCSV(csv, { hascomments = true })
+	assert(#rows == 3, "Should have 3 rows (comments filtered, header + 2 data rows)")
+	assert(rows[1][1] == "foo", "First row should be header row")
+	assert(rows[2][1] == "1", "Second row first field should be '1'")
+	assert(rows[3][1] == "4", "Third row first field should be '4'")
+end)
+
+-- Test fromCSV with comments and headers
+test("fromCSV with comments and headers", function()
+	local csv = "#mercenary_profiles\nId,Name,Value\n1,Test,100\n# End of data\n2,Test2,200"
+	local rows = fromCSV(csv, { hasheader = true, hascomments = true })
+	assert(#rows == 2, "Should have 2 data rows")
+	assert(rows[1].Id == "1", "First row Id should be '1'")
+	assert(rows[1].Name == "Test", "First row Name should be 'Test'")
+	assert(rows[1].Value == "100", "First row Value should be '100'")
+	assert(rows[2].Id == "2", "Second row Id should be '2'")
+end)
+
+-- Test fromCSV with comments disabled
+test("fromCSV without comments", function()
+	local csv = "# This should not be filtered\nfoo,bar\n1,2"
+	local rows = fromCSV(csv, { hascomments = false })
+	assert(#rows == 3, "Should have 3 rows (including comment)")
+	assert(rows[1][1] == "# This should not be filtered", "Comment line should be preserved")
+end)
+
+-- Test fromCSV with comment at start
+test("fromCSV comment at start", function()
+	local csv = "# Header comment\nId,Name\n1,Test"
+	local rows = fromCSV(csv, { hascomments = true })
+	assert(#rows == 2, "Should have 2 rows (comment filtered)")
+	assert(rows[1][1] == "Id", "First row should be header")
+end)
+
+-- Test fromCSV with comment with leading whitespace
+test("fromCSV comment with whitespace", function()
+	local csv = "  # Comment with spaces\nId,Name\n1,Test"
+	local rows = fromCSV(csv, { hascomments = true })
+	assert(#rows == 2, "Should have 2 rows (comment with spaces filtered)")
+	assert(rows[1][1] == "Id", "First row should be header")
+end)
+
+-- Test fromCSV with comment with tabs
+test("fromCSV comment with tabs", function()
+	local csv = "\t# Comment with tab\nId,Name\n1,Test"
+	local rows = fromCSV(csv, { hascomments = true })
+	assert(#rows == 2, "Should have 2 rows (comment with tab filtered)")
+	assert(rows[1][1] == "Id", "First row should be header")
+end)
+
+-- Test fromCSV with multiple consecutive comments
+test("fromCSV multiple consecutive comments", function()
+	local csv = "# First comment\n# Second comment\n# Third comment\nId,Name\n1,Test"
+	local rows = fromCSV(csv, { hascomments = true })
+	assert(#rows == 2, "Should have 2 rows (all comments filtered)")
+	assert(rows[1][1] == "Id", "First row should be header")
+end)
+
+-- Test fromCSV with comment in middle of data
+test("fromCSV comment in middle", function()
+	local csv = "Id,Name\n1,Test\n# Middle comment\n2,Test2"
+	local rows = fromCSV(csv, { hascomments = true })
+	assert(#rows == 3, "Should have 3 rows (comment filtered)")
+	assert(rows[1][1] == "Id", "First row should be header")
+	assert(rows[2][1] == "1", "Second row should be first data")
+	assert(rows[3][1] == "2", "Third row should be second data")
+end)
+
+-- Test fromCSV with comment at end
+test("fromCSV comment at end", function()
+	local csv = "Id,Name\n1,Test\n# End comment"
+	local rows = fromCSV(csv, { hascomments = true })
+	assert(#rows == 2, "Should have 2 rows (end comment filtered)")
+	assert(rows[1][1] == "Id", "First row should be header")
+	assert(rows[2][1] == "1", "Second row should be data")
+end)
+
+-- Test fromCSV with empty comment line
+test("fromCSV empty comment", function()
+	local csv = "#\nId,Name\n1,Test"
+	local rows = fromCSV(csv, { hascomments = true })
+	assert(#rows == 2, "Should have 2 rows (empty comment filtered)")
+	assert(rows[1][1] == "Id", "First row should be header")
+end)
+
+-- Test fromCSV with comment and headers
+test("fromCSV comment with headers enabled", function()
+	local csv = "#mercenary_profiles\nId,Name,Value\n1,Test,100\n2,Test2,200"
+	local rows = fromCSV(csv, { hasheader = true, hascomments = true })
+	assert(#rows == 2, "Should have 2 data rows")
+	assert(rows[1].Id == "1", "First row Id should be '1'")
+	assert(rows[1].Name == "Test", "First row Name should be 'Test'")
+	assert(rows[2].Id == "2", "Second row Id should be '2'")
+end)
+
+-- Test fromCSV with comment and TSV delimiter
+test("fromCSV comment with tab delimiter", function()
+	local csv = "# Comment\nId\tName\n1\tTest"
+	local rows = fromCSV(csv, { delimiter = "\t", hascomments = true })
+	assert(#rows == 2, "Should have 2 rows")
+	assert(rows[1][1] == "Id", "First row should be header")
+	assert(rows[2][1] == "1", "Second row first field should be '1'")
+end)
+
+-- Test fromCSV with comment and headers and TSV
+test("fromCSV comment with headers and TSV", function()
+	local csv = "#mercenary_profiles\nId\tName\tValue\n1\tTest\t100"
+	local rows = fromCSV(csv, { delimiter = "\t", hasheader = true, hascomments = true })
+	assert(#rows == 1, "Should have 1 data row")
+	assert(rows[1].Id == "1", "Row Id should be '1'")
+	assert(rows[1].Name == "Test", "Row Name should be 'Test'")
+	assert(rows[1].Value == "100", "Row Value should be '100'")
+end)
+
+-- Test fromCSV with data field starting with # (not a comment)
+test("fromCSV data field starting with hash", function()
+	local csv = "Id,Name\n1,#NotAComment\n2,Test"
+	local rows = fromCSV(csv, { hascomments = true })
+	assert(#rows == 3, "Should have 3 rows (data with # not filtered)")
+	assert(rows[1][1] == "Id", "First row should be header")
+	assert(rows[2][2] == "#NotAComment", "Second row should have #NotAComment as data")
+end)
+
+-- Test fromCSV with quoted field starting with #
+test("fromCSV quoted field with hash", function()
+	local csv = 'Id,Name\n1,"#NotAComment"\n2,Test'
+	local rows = fromCSV(csv, { hascomments = true })
+	assert(#rows == 3, "Should have 3 rows (quoted # not filtered)")
+	assert(rows[2][2] == "#NotAComment", "Quoted field with # should be preserved")
+end)
+
+-- Test fromCSV with comment after quoted field
+test("fromCSV comment after quoted field", function()
+	local csv = 'Id,Name\n1,"Test"\n# This is a comment\n2,Test2'
+	local rows = fromCSV(csv, { hascomments = true })
+	assert(#rows == 3, "Should have 3 rows (comment filtered)")
+	assert(rows[2][2] == "Test", "Quoted field should be preserved")
+	assert(rows[3][1] == "2", "Third row should be second data row")
+end)
+
+-- Math function tests
+test("min function", function()
+	assert(min(5, 3) == 3, "min(5, 3) should be 3")
+	assert(min(-1, 0) == -1, "min(-1, 0) should be -1")
+	assert(min(10, 10) == 10, "min(10, 10) should be 10")
+end)
+
+test("max function", function()
+	assert(max(5, 3) == 5, "max(5, 3) should be 5")
+	assert(max(-1, 0) == 0, "max(-1, 0) should be 0")
+	assert(max(10, 10) == 10, "max(10, 10) should be 10")
+end)
+
+test("round function", function()
+	assert(round(3.14159) == 3, "round(3.14159) should be 3")
+	assert(round(3.14159, 2) == 3.14, "round(3.14159, 2) should be 3.14")
+	assert(round(3.5) == 4, "round(3.5) should be 4")
+	assert(round(3.4) == 3, "round(3.4) should be 3")
+	assert(round(123.456, 1) == 123.5, "round(123.456, 1) should be 123.5")
+end)
+
+test("floor function", function()
+	assert(floor(3.7) == 3, "floor(3.7) should be 3")
+	assert(floor(-3.7) == -4, "floor(-3.7) should be -4")
+	assert(floor(5) == 5, "floor(5) should be 5")
+end)
+
+test("ceil function", function()
+	assert(ceil(3.2) == 4, "ceil(3.2) should be 4")
+	assert(ceil(-3.2) == -3, "ceil(-3.2) should be -3")
+	assert(ceil(5) == 5, "ceil(5) should be 5")
+end)
+
+-- String function tests
+test("upper function", function()
+	assert(upper("hello") == "HELLO", "upper('hello') should be 'HELLO'")
+	assert(upper("Hello World") == "HELLO WORLD", "upper('Hello World') should be 'HELLO WORLD'")
+	assert(upper("123abc") == "123ABC", "upper('123abc') should be '123ABC'")
+end)
+
+test("lower function", function()
+	assert(lower("HELLO") == "hello", "lower('HELLO') should be 'hello'")
+	assert(lower("Hello World") == "hello world", "lower('Hello World') should be 'hello world'")
+	assert(lower("123ABC") == "123abc", "lower('123ABC') should be '123abc'")
+end)
+
+test("format function", function()
+	assert(format("Hello %s", "World") == "Hello World", "format should work")
+	assert(format("Number: %d", 42) == "Number: 42", "format with number should work")
+	assert(format("%.2f", 3.14159) == "3.14", "format with float should work")
+end)
+
+test("trim function", function()
+	assert(trim("  hello  ") == "hello", "trim should remove leading and trailing spaces")
+	assert(trim("  hello world  ") == "hello world", "trim should preserve internal spaces")
+	assert(trim("hello") == "hello", "trim should not affect strings without spaces")
+	assert(trim("   ") == "", "trim should handle all spaces")
+end)
+
+test("strsplit function", function()
+	local result = strsplit("a,b,c", ",")
+	assert(#result == 3, "strsplit should return 3 elements")
+	assert(result[1] == "a", "First element should be 'a'")
+	assert(result[2] == "b", "Second element should be 'b'")
+	assert(result[3] == "c", "Third element should be 'c'")
+end)
+
+test("strsplit with default separator", function()
+	local result = strsplit("a b c")
+	assert(#result == 3, "strsplit with default should return 3 elements")
+	assert(result[1] == "a", "First element should be 'a'")
+	assert(result[2] == "b", "Second element should be 'b'")
+	assert(result[3] == "c", "Third element should be 'c'")
+end)
+
+test("strsplit with custom separator", function()
+	local result = strsplit("a|b|c", "|")
+	assert(#result == 3, "strsplit with pipe should return 3 elements")
+	assert(result[1] == "a", "First element should be 'a'")
+	assert(result[2] == "b", "Second element should be 'b'")
+	assert(result[3] == "c", "Third element should be 'c'")
+end)
+
+-- Conversion function tests
+test("num function", function()
+	assert(num("123") == 123, "num('123') should be 123")
+	assert(num("45.67") == 45.67, "num('45.67') should be 45.67")
+	assert(num("invalid") == 0, "num('invalid') should be 0")
+	assert(num("") == 0, "num('') should be 0")
+end)
+
+test("str function", function()
+	assert(str(123) == "123", "str(123) should be '123'")
+	assert(str(45.67) == "45.67", "str(45.67) should be '45.67'")
+	assert(str(0) == "0", "str(0) should be '0'")
+end)
+
+test("is_number function", function()
+	assert(is_number("123") == true, "is_number('123') should be true")
+	assert(is_number("45.67") == true, "is_number('45.67') should be true")
+	assert(is_number("invalid") == false, "is_number('invalid') should be false")
+	assert(is_number("") == false, "is_number('') should be false")
+	assert(is_number("123abc") == false, "is_number('123abc') should be false")
+end)
+
+-- Table function tests
+test("isArray function", function()
+	assert(isArray({ 1, 2, 3 }) == true, "isArray should return true for sequential array")
+	assert(isArray({ "a", "b", "c" }) == true, "isArray should return true for string array")
+	assert(isArray({}) == true, "isArray should return true for empty array")
+	assert(isArray({ a = 1, b = 2 }) == false, "isArray should return false for map")
+	assert(isArray({ 1, 2, [4] = 4 }) == false, "isArray should return false for sparse array")
+	assert(
+		isArray({ [1] = 1, [2] = 2, [3] = 3 }) == true,
+		"isArray should return true for 1-indexed array"
+	)
+	assert(
+		isArray({ [0] = 1, [1] = 2 }) == false,
+		"isArray should return false for 0-indexed array"
+	)
+	assert(
+		isArray({ [1] = 1, [2] = 2, [4] = 4 }) == false,
+		"isArray should return false for non-sequential array"
+	)
+	assert(isArray("not a table") == false, "isArray should return false for non-table")
+	assert(isArray(123) == false, "isArray should return false for number")
+end)
+
+test("fromCSV assigns header keys correctly", function()
+	local teststr = [[
+#mercenary_profiles
+Id	ModifyStartCost	ModifyStep	ModifyLevelLimit	Health	ResistSheet	WoundSlots	MeleeDamage	MeleeAccuracy	RangeAccuracy	ReceiveAmputationChance	ReceiveWoundChanceMult	AttackWoundChanceMult	Dodge	Los	StarvationLimit	PainThresholdLimit	PainThresholdRegen	TalentPerkId	ActorId	SkinIndex	HairType	HairColorHex	VoiceBank	Immunity	CreatureClass
+john_hawkwood_boss	20	0.1		140	blunt 0 pierce 0 lacer 0 fire 0 cold 0 poison 0 shock 0 beam 0	HumanHead HumanShoulder HumanArm HumanThigh HumanFeet HumanChest HumanBody HumanStomach HumanKnee	blunt 8 16 crit 1.60 critchance 0.05	0.5	0.5	0.03	0.5	1.2	0.3	8	2200	16	2	talent_the_man_who_sold_the_world	human_male	0	hair1	#633D08	player		Human
+francis_reid_daly	20	0.1		130	blunt 0 pierce 0 lacer 0 fire 0 cold 0 poison 0 shock 0 beam 0	HumanHead HumanShoulder HumanArm HumanThigh HumanFeet HumanChest HumanBody HumanStomach HumanKnee	blunt 7 14 crit 1.70 critchance 0.05	0.5	0.4	0.04	0.9	1	0.3	8	2000	10	1	talent_weapon_durability	human_male	0			player		Human
+]]
+	local rows = fromCSV(teststr, { delimiter = "\t", hasheader = true, hascomments = true })
+	assert(#rows == 2, "Should have 2 data rows")
+
+	-- Test first row
+	assert(rows[1].Id == "john_hawkwood_boss", "First row Id should be 'john_hawkwood_boss'")
+	assert(rows[1].ModifyStartCost == "20", "First row ModifyStartCost should be '20'")
+	assert(rows[1].ModifyStep == "0.1", "First row ModifyStep should be '0.1'")
+	assert(rows[1].Health == "140", "First row Health should be '140'")
+	assert(rows[1].ActorId == "human_male", "First row ActorId should be 'human_male'")
+	assert(rows[1].HairColorHex == "#633D08", "First row HairColorHex should be '#633D08'")
+
+	-- Test second row
+	assert(rows[2].Id == "francis_reid_daly", "Second row Id should be 'francis_reid_daly'")
+	assert(rows[2].ModifyStartCost == "20", "Second row ModifyStartCost should be '20'")
+	assert(rows[2].ModifyStep == "0.1", "Second row ModifyStep should be '0.1'")
+	assert(rows[2].Health == "130", "Second row Health should be '130'")
+	assert(rows[2].ActorId == "human_male", "Second row ActorId should be 'human_male'")
+
+	-- Test that numeric indices still work
+	assert(rows[1][1] == "john_hawkwood_boss", "First row first field by index should work")
+	assert(rows[1][2] == "20", "First row second field by index should work")
+end)
+
+test("fromCSV debug header assignment", function()
+	local csv = "Id	Name	Value\n1	Test	100\n2	Test2	200"
+	local rows = fromCSV(csv, { delimiter = "\t", hasheader = true })
+	assert(rows[1].Id == "1", "Id should be '1'")
+	assert(rows[1].Name == "Test", "Name should be 'Test'")
+	assert(rows[1].Value == "100", "Value should be '100'")
+end)
+
+test("fromCSV real world mercenary file format", function()
+	local csv = [[#mercenary_profiles
+Id	ModifyStartCost	ModifyStep	ModifyLevelLimit	Health	ResistSheet	WoundSlots	MeleeDamage	MeleeAccuracy	RangeAccuracy	ReceiveAmputationChance	ReceiveWoundChanceMult	AttackWoundChanceMult	Dodge	Los	StarvationLimit	PainThresholdLimit	PainThresholdRegen	TalentPerkId	ActorId	SkinIndex	HairType	HairColorHex	VoiceBank	Immunity	CreatureClass
+john_hawkwood_boss	20	0.1		140	blunt 0 pierce 0 lacer 0 fire 0 cold 0 poison 0 shock 0 beam 0	HumanHead HumanShoulder HumanArm HumanThigh HumanFeet HumanChest HumanBody HumanStomach HumanKnee	blunt 8 16 crit 1.60 critchance 0.05	0.5	0.5	0.03	0.5	1.2	0.3	8	2200	16	2	talent_the_man_who_sold_the_world	human_male	0	hair1	#633D08	player		Human
+francis_reid_daly	20	0.1		130	blunt 0 pierce 0 lacer 0 fire 0 cold 0 poison 0 shock 0 beam 0	HumanHead HumanShoulder HumanArm HumanThigh HumanFeet HumanChest HumanBody HumanStomach HumanKnee	blunt 7 14 crit 1.70 critchance 0.05	0.5	0.4	0.04	0.9	1	0.3	8	2000	10	1	talent_weapon_durability	human_male	0			player		Human
+]]
+	local rows = fromCSV(csv, { delimiter = "\t", hasheader = true, hascomments = true })
+	assert(#rows == 2, "Should have 2 data rows")
+
+	assert(rows[1].Id == "john_hawkwood_boss", "First row Id should be 'john_hawkwood_boss'")
+	assert(rows[1].ModifyStartCost == "20", "First row ModifyStartCost should be '20'")
+	assert(rows[2].Id == "francis_reid_daly", "Second row Id should be 'francis_reid_daly'")
+end)
+
+test("full CSV parser complex", function()
+	local original = [[
+#mercenary_profiles																									
+Id	ModifyStartCost	ModifyStep	ModifyLevelLimit	Health	ResistSheet	WoundSlots	MeleeDamage	MeleeAccuracy	RangeAccuracy	ReceiveAmputationChance	ReceiveWoundChanceMult	AttackWoundChanceMult	Dodge	Los	StarvationLimit	PainThresholdLimit	PainThresholdRegen	TalentPerkId	ActorId	SkinIndex	HairType	HairColorHex	VoiceBank	Immunity	CreatureClass
+john_hawkwood_boss	20	0.1		140	blunt 0 pierce 0 lacer 0 fire 0 cold 0 poison 0 shock 0 beam 0	HumanHead HumanShoulder HumanArm HumanThigh HumanFeet HumanChest HumanBody HumanStomach HumanKnee	blunt 8 16 crit 1.60 critchance 0.05	0.5	0.5	0.03	0.5	1.2	0.3	8	2200	16	2	talent_the_man_who_sold_the_world	human_male	0	hair1	#633D08	player		Human
+francis_reid_daly	20	0.1		130	blunt 0 pierce 0 lacer 0 fire 0 cold 0 poison 0 shock 0 beam 0	HumanHead HumanShoulder HumanArm HumanThigh HumanFeet HumanChest HumanBody HumanStomach HumanKnee	blunt 7 14 crit 1.70 critchance 0.05	0.5	0.4	0.04	0.9	1	0.3	8	2000	10	1	talent_weapon_durability	human_male	0			player		Human
+victoria_boudicca	20	0.1		90	blunt 0 pierce 0 lacer 0 fire 0 cold 0 poison 0 shock 0 beam 0	HumanHead HumanShoulder HumanArm HumanThigh HumanFeet HumanChest HumanBody HumanStomach HumanKnee	blunt 5 10 crit 1.70 critchance 0.1	0.4	0.45	0.05	1	1.2	0.3	8	1800	8	1	talent_weapon_distance	human_female	0	hair1	#633D08	player		Human
+persival_fawcett	20	0.1		150	blunt 0 pierce 0 lacer 0 fire 0 cold 0 poison 0 shock 0 beam 0	HumanHead HumanShoulder HumanArm HumanThigh HumanFeet HumanChest HumanBody HumanStomach HumanKnee	blunt 6 12 crit 1.70 critchance 0.05	0.5	0.35	0.05	0.6	1	0.25	8	2100	16	1	talent_all_resists	human_male	1	hair1	#633D08	player		Human
+Isabella_capet	20	0.1		100	blunt 0 pierce 0 lacer 0 fire 0 cold 0 poison 0 shock 0 beam 0	HumanHead HumanShoulder HumanArm HumanThigh HumanFeet HumanChest HumanBody HumanStomach HumanKnee	blunt 7 14 crit 1.70 critchance 0.15	0.55	0.3	0.03	0.8	1.4	0.35	7	1700	14	2	talent_ignore_infection	human_female	1	hair3	#FF3100	player		Human
+maximilian_rohr	20	0.1		120	blunt 0 pierce 0 lacer 0 fire 0 cold 0 poison 0 shock 0 beam 0	HumanHead HumanShoulder HumanArm HumanThigh HumanFeet HumanChest HumanBody HumanStomach HumanKnee	blunt 8 16 crit 1.75 critchance 0.05	0.45	0.45	0.06	0.9	1	0.2	8	2000	14	1	talent_ignore_pain	human_male	0	hair2	#FFC400	player		Human
+priya_marlon	20	0.1		110	blunt 0 pierce 0 lacer 0 fire 0 cold 0 poison 0 shock 0 beam 0	HumanHead HumanShoulder HumanArm HumanThigh HumanFeet HumanChest HumanBody HumanStomach HumanKnee	blunt 5 10 crit 1.70 critchance 0.15	0.45	0.35	0.05	1	1.1	0.3	7	2200	12	1	talent_all_consumables_stack	human_female	0	hair2	#FFC400	player		Human
+jacques_kennet	20	0.1		120	blunt 0 pierce 0 lacer 0 fire 0 cold 0 poison 0 shock 0 beam 0	HumanHead HumanShoulder HumanArm HumanThigh HumanFeet HumanChest HumanBody HumanStomach HumanKnee	blunt 5 10 crit 1.70 critchance 0.05	0.45	0.35	0.04	0.9	1.2	0.3	8	2300	10	1	talent_reload_time	human_male	0	hair1	#908E87	player		Human
+mirza_aishatu	20	0.1		110	blunt 0 pierce 0 lacer 0 fire 0 cold 0 poison 0 shock 0 beam 0	HumanHead HumanShoulder HumanArm HumanThigh HumanFeet HumanChest HumanBody HumanStomach HumanKnee	blunt 7 14 crit 1.70 critchance 0.05	0.55	0.45	0.03	1	1.1	0.25	9	2000	10	1	talent_starving_slower	human_female	1	hair2	#633D08	player		Human
+kenzie_yukio	20	0.1		100	blunt 0 pierce 0 lacer 0 fire 0 cold 0 poison 0 shock 0 beam 0	HumanHead HumanShoulder HumanArm HumanThigh HumanFeet HumanChest HumanBody HumanStomach HumanKnee	blunt 5 10 crit 1.70 critchance 0.1	0.6	0.4	0.04	1	1	0.4	7	1600	12	1	talent_weight_dodge_affect	human_male	0	hair2	#633D08	player		Human
+marika_wulfnod	20	0.1		100	blunt 0 pierce 0 lacer 0 fire 0 cold 0 poison 0 shock 0 beam 0	HumanHead HumanShoulder HumanArm HumanThigh HumanFeet HumanChest HumanBody HumanStomach HumanKnee	blunt 6 12 crit 1.60 critchance 0.05	0.5	0.5	0.04	1	1	0.3	9	1900	12	1	talent_belt_slots	human_female	0	hair1	#FFC400	player		Human
+auberon_lukas	20	0.1		120	blunt 0 pierce 0 lacer 0 fire 0 cold 0 poison 0 shock 0 beam 0	HumanHead HumanShoulder HumanArm HumanThigh HumanFeet HumanChest HumanBody HumanStomach HumanKnee	blunt 4 8 crit 1.60 critchance 0.15	0.45	0.45	0.05	0.8	1	0.2	9	1900	8	2	talent_weapon_slot	human_male	0	hair2	#633D08	player		Human
+niko_medich	20	0.1		120	blunt 0 pierce 0 lacer 0 fire 0 cold 0 poison 0 shock 0 beam 0	HumanHead HumanShoulder HumanArm HumanThigh HumanFeet HumanChest HumanBody HumanStomach HumanKnee	blunt 5 10 crit 1.70 critchance 0.05	0.4	0.45	0.04	1	1.3	0.25	8	2000	10	1	talent_pistol_acc	human_male	0	hair1	#908E87	player		Human
+#end																									
+																									
+#mercenary_classes																									
+Id	ModifyStartCost	ModifyStep	PerkIds																						
+scouts_of_hades	30	0.1	cqc_specialist_basic military_training_basic gear_maintenance_basic blind_fury_basic fire_transfer_basic assault_reflex_basic																						
+ecclipse_blades	30	0.1	berserkgang_basic athletics_basic reaction_training_basic cold_weapon_wielding_basic cannibalism_basic carnage_basic																						
+tifton_elite	30	0.1	heavy_weaponary_basic grenadier_basic selfhealing_basic stationary_defense_basic spray_and_pray_basic shock_awe_basic																						
+tunnel_rats	30	0.1	cautious_basic handmade_shotgun_ammo_basic marauder_basic dirty_shot_basic vicious_symbiosis_basic covermaster_basic																						
+phoenix_brigade	30	0.1	shielding_basic battle_physicist_basic reinforced_battery_basic revealing_flame_basic cauterize_basic scholar_basic																						
+]]
+
+	-- Parse with headers and comments
+	local rows = fromCSV(original, { delimiter = "\t", hasheader = true, hascomments = true })
+	assert(#rows > 0, "Should have parsed rows")
+
+	-- Convert back to CSV with headers
+	local csv = toCSV(rows, { delimiter = "\t", hasheader = true })
+
+	-- Parse again
+	local rows2 = fromCSV(csv, { delimiter = "\t", hasheader = true, hascomments = false })
+
+	-- Verify identical - same number of rows
+	assert(#rows2 == #rows, "Round trip should have same number of rows")
+
+	-- Verify first row data is identical
+	assert(rows2[1].Id == rows[1].Id, "Round trip first row Id should match")
+	assert(
+		rows2[1].ModifyStartCost == rows[1].ModifyStartCost,
+		"Round trip first row ModifyStartCost should match"
+	)
+	assert(rows2[1].Health == rows[1].Health, "Round trip first row Health should match")
+
+	-- Verify headers are preserved
+	assert(rows2.Headers ~= nil, "Round trip rows should have Headers field")
+	assert(#rows2.Headers == #rows.Headers, "Headers should have same number of elements")
+	assert(rows2.Headers[1] == rows.Headers[1], "First header should match")
+end)
+
+-- Test metatable: row[1] and row.foobar return same value
+test("metatable row[1] equals row.header", function()
+	local csv = "Id	Name	Value\n1	Test	100"
+	local rows = fromCSV(csv, { delimiter = "\t", hasheader = true })
+	assert(rows[1][1] == rows[1].Id, "row[1] should equal row.Id")
+	assert(rows[1][2] == rows[1].Name, "row[2] should equal row.Name")
+	assert(rows[1][3] == rows[1].Value, "row[3] should equal row.Value")
+	assert(rows[1].Id == "1", "row.Id should be '1'")
+	assert(rows[1][1] == "1", "row[1] should be '1'")
+end)
+
+-- Test metatable: setting via header name updates numeric index
+test("metatable set via header name", function()
+	local csv = "Id	Name	Value\n1	Test	100"
+	local rows = fromCSV(csv, { delimiter = "\t", hasheader = true })
+	rows[1].Id = "999"
+	assert(rows[1][1] == "999", "Setting row.Id should update row[1]")
+	assert(rows[1].Id == "999", "row.Id should be '999'")
+end)
+
+-- Test metatable: error on unknown header assignment
+test("metatable error on unknown header", function()
+	local csv = "Id	Name	Value\n1	Test	100"
+	local rows = fromCSV(csv, { delimiter = "\t", hasheader = true })
+	local ok, errMsg = pcall(function() rows[1].UnknownHeader = "test" end)
+	assert(ok == false, "Should error on unknown header")
+	assert(string.find(errMsg, "unknown header"), "Error should mention unknown header")
+end)
+
+-- Test metatable: numeric indices still work
+test("metatable numeric indices work", function()
+	local csv = "Id	Name	Value\n1	Test	100"
+	local rows = fromCSV(csv, { delimiter = "\t", hasheader = true })
+	rows[1][1] = "999"
+	assert(rows[1].Id == "999", "Setting row[1] should update row.Id")
+	assert(rows[1][1] == "999", "row[1] should be '999'")
+end)
+
+-- Test metatable: numeric keys work normally
+test("metatable numeric keys work", function()
+	local csv = "Id	Name	Value\n1	Test	100"
+	local rows = fromCSV(csv, { delimiter = "\t", hasheader = true })
+	rows[1][100] = "hundred"
+	assert(rows[1][100] == "hundred", "Numeric keys should work")
+end)
+
+print("\nAll tests completed!")

processor/luahelper.lua

@@ -0,0 +1,624 @@
+-- Custom Lua helpers for math operations
+
+--- Returns the minimum of two numbers
+--- @param a number First number
+--- @param b number Second number
+--- @return number Minimum value
+function min(a, b) return math.min(a, b) end
+
+--- Returns the maximum of two numbers
+--- @param a number First number
+--- @param b number Second number
+--- @return number Maximum value
+function max(a, b) return math.max(a, b) end
+
+--- Rounds a number to n decimal places
+--- @param x number Number to round
+--- @param n number? Number of decimal places (default: 0)
+--- @return number Rounded number
+function round(x, n)
+	if n == nil then n = 0 end
+	return math.floor(x * 10 ^ n + 0.5) / 10 ^ n
+end
+
+--- Returns the floor of a number
+--- @param x number Number to floor
+--- @return number Floored number
+function floor(x) return math.floor(x) end
+
+--- Returns the ceiling of a number
+--- @param x number Number to ceil
+--- @return number Ceiled number
+function ceil(x) return math.ceil(x) end
+
+--- Converts string to uppercase
+--- @param s string String to convert
+--- @return string Uppercase string
+function upper(s) return string.upper(s) end
+
+--- Converts string to lowercase
+--- @param s string String to convert
+--- @return string Lowercase string
+function lower(s) return string.lower(s) end
+
+--- Formats a string using Lua string.format
+--- @param s string Format string
+--- @param ... any Values to format
+--- @return string Formatted string
+function format(s, ...) return string.format(s, ...) end
+
+--- Removes leading and trailing whitespace from string
+--- @param s string String to trim
+--- @return string Trimmed string
+function trim(s) return string.gsub(s, "^%s*(.-)%s*$", "%1") end
+
+--- Splits a string by separator
+--- @param inputstr string String to split
+--- @param sep string? Separator pattern (default: whitespace)
+--- @return table Array of string parts
+function strsplit(inputstr, sep)
+	if sep == nil then sep = "%s" end
+	local t = {}
+	for str in string.gmatch(inputstr, "([^" .. sep .. "]+)") do
+		table.insert(t, str)
+	end
+	return t
+end
+
+---@param table table
+---@param depth number?
+function dump(table, depth)
+	if depth == nil then depth = 0 end
+	if depth > 200 then
+		print("Error: Depth > 200 in dump()")
+		return
+	end
+	for k, v in pairs(table) do
+		if type(v) == "table" then
+			print(string.rep("  ", depth) .. k .. ":")
+			dump(v, depth + 1)
+		else
+			print(string.rep("  ", depth) .. k .. ": ", v)
+		end
+	end
+end
+
+--- @class ParserOptions
+--- @field delimiter string? The field delimiter (default: ",").
+--- @field hasheader boolean? If true, first non-comment row is treated as headers (default: false).
+--- @field hascomments boolean? If true, lines starting with '#' are skipped (default: false).
+
+--- @type ParserOptions
+parserDefaultOptions = { delimiter = ",", hasheader = false, hascomments = false }
+
+--- Validates options against a set of valid option keys.
+--- @param options ParserOptions? The options table to validate
+function areOptionsValid(options)
+	if options == nil then return end
+
+	if type(options) ~= "table" then error("options must be a table") end
+
+	-- Build valid options list from validOptions table
+	local validOptionsStr = ""
+	for k, _ in pairs(parserDefaultOptions) do
+		validOptionsStr = validOptionsStr .. k .. ", "
+	end
+
+	for k, _ in pairs(options) do
+		if parserDefaultOptions[k] == nil then
+			error(
+				"unknown option: " .. tostring(k) .. " (valid options: " .. validOptionsStr .. ")"
+			)
+		end
+	end
+end
+
+--- Parses CSV text into rows and fields using a minimal RFC 4180 state machine.
+---
+--- Requirements/assumptions:
+--- - Input is a single string containing the entire CSV content.
+--- - Field separators are specified by delimiter option (default: comma).
+--- - Newlines between rows may be "\n" or "\r\n". "\r\n" is treated as one line break.
+--- - Fields may be quoted with double quotes (").
+--- - Inside quoted fields, doubled quotes ("") represent a literal quote character.
+--- - No backslash escaping is supported (not part of RFC 4180).
+--- - Newlines inside quoted fields are preserved as part of the field.
+--- - Leading/trailing spaces are preserved; no trimming is performed.
+--- - Empty fields and empty rows are preserved.
+--- - The final row is emitted even if the text does not end with a newline.
+--- - Lines starting with '#' (after optional leading whitespace) are treated as comments and skipped if hascomments is true.
+---
+--- @param csv string The CSV text to parse.
+--- @param options ParserOptions? Options for the parser
+--- @return table #A table (array) of rows; each row is a table with numeric indices and optionally header-named keys.
+function fromCSV(csv, options)
+	if options == nil then options = {} end
+
+	-- Validate options
+	areOptionsValid(options)
+
+	local delimiter = options.delimiter or parserDefaultOptions.delimiter
+	local hasheader = options.hasheader or parserDefaultOptions.hasheader
+	local hascomments = options.hascomments or parserDefaultOptions.hascomments
+
+	local allRows = {}
+	local fields = {}
+	local field = {}
+
+	local STATE_DEFAULT = 1
+	local STATE_IN_QUOTES = 2
+	local STATE_QUOTE_IN_QUOTES = 3
+	local state = STATE_DEFAULT
+
+	local i = 1
+	local len = #csv
+
+	while i <= len do
+		local c = csv:sub(i, i)
+
+		if state == STATE_DEFAULT then
+			if c == '"' then
+				state = STATE_IN_QUOTES
+				i = i + 1
+			elseif c == delimiter then
+				table.insert(fields, table.concat(field))
+				field = {}
+				i = i + 1
+			elseif c == "\r" or c == "\n" then
+				table.insert(fields, table.concat(field))
+				field = {}
+				local shouldAdd = true
+				if hascomments and #fields > 0 then
+					local firstField = fields[1]
+					local trimmed = trim(firstField)
+					if string.sub(trimmed, 1, 1) == "#" then shouldAdd = false end
+				end
+				if shouldAdd then table.insert(allRows, fields) end
+				fields = {}
+				if c == "\r" and i < len and csv:sub(i + 1, i + 1) == "\n" then
+					i = i + 2
+				else
+					i = i + 1
+				end
+			else
+				table.insert(field, c)
+				i = i + 1
+			end
+		elseif state == STATE_IN_QUOTES then
+			if c == '"' then
+				state = STATE_QUOTE_IN_QUOTES
+				i = i + 1
+			else
+				table.insert(field, c)
+				i = i + 1
+			end
+		else -- STATE_QUOTE_IN_QUOTES
+			if c == '"' then
+				table.insert(field, '"')
+				state = STATE_IN_QUOTES
+				i = i + 1
+			elseif c == delimiter then
+				table.insert(fields, table.concat(field))
+				field = {}
+				state = STATE_DEFAULT
+				i = i + 1
+			elseif c == "\r" or c == "\n" then
+				table.insert(fields, table.concat(field))
+				field = {}
+				local shouldAdd = true
+				if hascomments and #fields > 0 then
+					local firstField = fields[1]
+					local trimmed = string.gsub(firstField, "^%s*(.-)%s*$", "%1")
+					if string.sub(trimmed, 1, 1) == "#" then shouldAdd = false end
+				end
+				if shouldAdd then table.insert(allRows, fields) end
+				fields = {}
+				state = STATE_DEFAULT
+				if c == "\r" and i < len and csv:sub(i + 1, i + 1) == "\n" then
+					i = i + 2
+				else
+					i = i + 1
+				end
+			else
+				state = STATE_DEFAULT
+				-- Don't increment i, reprocess character in DEFAULT state
+			end
+		end
+	end
+
+	if #field > 0 or #fields > 0 then
+		table.insert(fields, table.concat(field))
+		local shouldAdd = true
+		if hascomments and #fields > 0 then
+			local firstField = fields[1]
+			local trimmed = string.gsub(firstField, "^%s*(.-)%s*$", "%1")
+			if string.sub(trimmed, 1, 1) == "#" then shouldAdd = false end
+		end
+		if shouldAdd then table.insert(allRows, fields) end
+	end
+
+	if hasheader and #allRows > 0 then
+		local headers = allRows[1]
+		local headerMap = {}
+		for j = 1, #headers do
+			if headers[j] ~= nil and headers[j] ~= "" then
+				local headerName = trim(headers[j])
+				headerMap[headerName] = j
+			end
+		end
+
+		local header_mt = {
+			headers = headerMap,
+			__index = function(t, key)
+				local mt = getmetatable(t)
+				if type(key) == "string" and mt.headers and mt.headers[key] then
+					return rawget(t, mt.headers[key])
+				end
+				return rawget(t, key)
+			end,
+			__newindex = function(t, key, value)
+				local mt = getmetatable(t)
+				if type(key) == "string" and mt.headers then
+					if mt.headers[key] then
+						rawset(t, mt.headers[key], value)
+					else
+						error("unknown header: " .. tostring(key))
+					end
+				else
+					rawset(t, key, value)
+				end
+			end,
+		}
+
+		local rows = {}
+		for ii = 2, #allRows do
+			local row = {}
+			local dataRow = allRows[ii]
+			for j = 1, #dataRow do
+				row[j] = dataRow[j]
+			end
+			setmetatable(row, header_mt)
+			table.insert(rows, row)
+		end
+		rows.Headers = headers
+		return rows
+	end
+
+	return allRows
+end
+
+--- Converts a table of rows back to CSV text format (RFC 4180 compliant).
+---
+--- Requirements:
+--- - Input is a table (array) of rows, where each row is a table (array) of field values.
+--- - Field values are converted to strings using tostring().
+--- - Fields are quoted if they contain the delimiter, newlines, or double quotes.
+--- - Double quotes inside quoted fields are doubled ("").
+--- - Fields are joined with the specified delimiter; rows are joined with newlines.
+--- - If includeHeaders is true and rows have a Headers field, headers are included as the first row.
+---
+--- @param rows table Array of rows, where each row is an array of field values.
+--- @param options ParserOptions? Options for the parser
+--- @return string #CSV-formatted text
+function toCSV(rows, options)
+	if options == nil then options = {} end
+
+	-- Validate options
+	areOptionsValid(options)
+
+	local delimiter = options.delimiter or parserDefaultOptions.delimiter
+	local includeHeaders = options.hasheader or parserDefaultOptions.hasheader
+	local rowStrings = {}
+
+	-- Include headers row if requested and available
+	if includeHeaders and #rows > 0 and rows.Headers ~= nil then
+		local headerStrings = {}
+		for _, header in ipairs(rows.Headers) do
+			local headerStr = tostring(header)
+			local needsQuoting = false
+			if
+				headerStr:find(delimiter)
+				or headerStr:find("\n")
+				or headerStr:find("\r")
+				or headerStr:find('"')
+			then
+				needsQuoting = true
+			end
+			if needsQuoting then
+				headerStr = headerStr:gsub('"', '""')
+				headerStr = '"' .. headerStr .. '"'
+			end
+			table.insert(headerStrings, headerStr)
+		end
+		table.insert(rowStrings, table.concat(headerStrings, delimiter))
+	end
+
+	for _, row in ipairs(rows) do
+		local fieldStrings = {}
+
+		for _, field in ipairs(row) do
+			local fieldStr = tostring(field)
+			local needsQuoting = false
+
+			if
+				fieldStr:find(delimiter)
+				or fieldStr:find("\n")
+				or fieldStr:find("\r")
+				or fieldStr:find('"')
+			then
+				needsQuoting = true
+			end
+
+			if needsQuoting then
+				fieldStr = fieldStr:gsub('"', '""')
+				fieldStr = '"' .. fieldStr .. '"'
+			end
+
+			table.insert(fieldStrings, fieldStr)
+		end
+
+		table.insert(rowStrings, table.concat(fieldStrings, delimiter))
+	end
+
+	return table.concat(rowStrings, "\n")
+end
+
+--- Converts string to number, returns 0 if invalid
+--- @param str string String to convert
+--- @return number Numeric value or 0
+function num(str) return tonumber(str) or 0 end
+
+--- Converts number to string
+--- @param num number Number to convert
+--- @return string String representation
+function str(num) return tostring(num) end
+
+--- Checks if string is numeric
+--- @param str string String to check
+--- @return boolean True if string is numeric
+function is_number(str) return tonumber(str) ~= nil end
+
+--- Checks if table is a sequential array (1-indexed with no gaps)
+--- @param t table Table to check
+--- @return boolean True if table is an array
+function isArray(t)
+	if type(t) ~= "table" then return false end
+	local max = 0
+	local count = 0
+	for k, _ in pairs(t) do
+		if type(k) ~= "number" or k < 1 or math.floor(k) ~= k then return false end
+		max = math.max(max, k)
+		count = count + 1
+	end
+	return max == count
+end
+
+modified = false
+
+-- ============================================================================
+-- XML HELPER FUNCTIONS
+-- ============================================================================
+
+--- Find all elements with a specific tag name (recursive search)
+--- @param root table The root XML element (with _tag, _attr, _children fields)
+--- @param tagName string The tag name to search for
+--- @return table Array of matching elements
+function findElements(root, tagName)
+	local results = {}
+
+	local function search(element)
+		if element._tag == tagName then table.insert(results, element) end
+		if element._children then
+			for _, child in ipairs(element._children) do
+				search(child)
+			end
+		end
+	end
+
+	search(root)
+	return results
+end
+
+--- Visit all elements recursively and call a function on each
+--- @param root table The root XML element
+--- @param callback function Function to call with each element: callback(element, depth, path)
+function visitElements(root, callback)
+	local function visit(element, depth, path)
+		callback(element, depth, path)
+		if element._children then
+			for i, child in ipairs(element._children) do
+				local childPath = path .. "/" .. child._tag .. "[" .. i .. "]"
+				visit(child, depth + 1, childPath)
+			end
+		end
+	end
+	visit(root, 0, "/" .. root._tag)
+end
+
+--- Get numeric value from XML element attribute
+--- @param element table XML element with _attr field
+--- @param attrName string Attribute name
+--- @return number|nil The numeric value or nil if not found/not numeric
+function getNumAttr(element, attrName)
+	if not element._attr then return nil end
+	local value = element._attr[attrName]
+	if not value then return nil end
+	return tonumber(value)
+end
+
+--- Set numeric value to XML element attribute
+--- @param element table XML element with _attr field
+--- @param attrName string Attribute name
+--- @param value number Numeric value to set
+function setNumAttr(element, attrName, value)
+	if not element._attr then element._attr = {} end
+	element._attr[attrName] = tostring(value)
+end
+
+--- Modify numeric attribute by applying a function
+--- @param element table XML element
+--- @param attrName string Attribute name
+--- @param func function Function that takes current value and returns new value
+--- @return boolean True if modification was made
+function modifyNumAttr(element, attrName, func)
+	local current = getNumAttr(element, attrName)
+	if current then
+		setNumAttr(element, attrName, func(current))
+		return true
+	end
+	return false
+end
+
+--- Find all elements matching a predicate function
+--- @param root table The root XML element
+--- @param predicate function Function that takes element and returns true/false
+--- @return table Array of matching elements
+function filterElements(root, predicate)
+	local results = {}
+	visitElements(root, function(element)
+		if predicate(element) then table.insert(results, element) end
+	end)
+	return results
+end
+
+--- Get text content of an element
+--- @param element table XML element
+--- @return string|nil The text content or nil
+function getText(element) return element._text end
+
+--- Set text content of an element
+--- @param element table XML element
+--- @param text string Text content to set
+function setText(element, text) element._text = text end
+
+--- Check if element has an attribute
+--- @param element table XML element
+--- @param attrName string Attribute name
+--- @return boolean True if attribute exists
+function hasAttr(element, attrName) return element._attr and element._attr[attrName] ~= nil end
+
+--- Get attribute value as string
+--- @param element table XML element
+--- @param attrName string Attribute name
+--- @return string|nil The attribute value or nil
+function getAttr(element, attrName)
+	if not element._attr then return nil end
+	return element._attr[attrName]
+end
+
+--- Set attribute value
+--- @param element table XML element
+--- @param attrName string Attribute name
+--- @param value any Value to set (will be converted to string)
+function setAttr(element, attrName, value)
+	if not element._attr then element._attr = {} end
+	element._attr[attrName] = tostring(value)
+end
+
+--- Find first element with a specific tag name (searches direct children only)
+--- @param parent table The parent XML element
+--- @param tagName string The tag name to search for
+--- @return table|nil The first matching element or nil
+function findFirstElement(parent, tagName)
+	if not parent._children then return nil end
+	for _, child in ipairs(parent._children) do
+		if child._tag == tagName then return child end
+	end
+	return nil
+end
+
+--- Add a child element to a parent
+--- @param parent table The parent XML element
+--- @param child table The child element to add
+function addChild(parent, child)
+	if not parent._children then parent._children = {} end
+	table.insert(parent._children, child)
+end
+
+--- Remove all children with a specific tag name
+--- @param parent table The parent XML element
+--- @param tagName string The tag name to remove
+--- @return number Count of removed children
+function removeChildren(parent, tagName)
+	if not parent._children then return 0 end
+	local removed = 0
+	local i = 1
+	while i <= #parent._children do
+		if parent._children[i]._tag == tagName then
+			table.remove(parent._children, i)
+			removed = removed + 1
+		else
+			i = i + 1
+		end
+	end
+	return removed
+end
+
+--- Get all direct children with a specific tag name
+--- @param parent table The parent XML element
+--- @param tagName string The tag name to search for
+--- @return table Array of matching children
+function getChildren(parent, tagName)
+	local results = {}
+	if not parent._children then return results end
+	for _, child in ipairs(parent._children) do
+		if child._tag == tagName then table.insert(results, child) end
+	end
+	return results
+end
+
+--- Count children with a specific tag name
+--- @param parent table The parent XML element
+--- @param tagName string The tag name to count
+--- @return number Count of matching children
+function countChildren(parent, tagName)
+	if not parent._children then return 0 end
+	local count = 0
+	for _, child in ipairs(parent._children) do
+		if child._tag == tagName then count = count + 1 end
+	end
+	return count
+end
+
+-- ============================================================================
+-- JSON HELPER FUNCTIONS
+-- ============================================================================
+
+--- Recursively visit all values in a JSON structure
+--- @param data table JSON data (nested tables)
+--- @param callback function Function called with (value, key, parent)
+function visitJSON(data, callback)
+	local function visit(obj, key, parent)
+		callback(obj, key, parent)
+		if type(obj) == "table" then
+			for k, v in pairs(obj) do
+				visit(v, k, obj)
+			end
+		end
+	end
+	visit(data, nil, nil)
+end
+
+--- Find all values in JSON matching a predicate
+--- @param data table JSON data
+--- @param predicate function Function that takes (value, key, parent) and returns true/false
+--- @return table Array of matching values
+function findInJSON(data, predicate)
+	local results = {}
+	visitJSON(data, function(value, key, parent)
+		if predicate(value, key, parent) then table.insert(results, value) end
+	end)
+	return results
+end
+
+--- Modify all numeric values in JSON matching a condition
+--- @param data table JSON data
+--- @param predicate function Function that takes (value, key, parent) and returns true/false
+--- @param modifier function Function that takes current value and returns new value
+function modifyJSONNumbers(data, predicate, modifier)
+	visitJSON(data, function(value, key, parent)
+		if type(value) == "number" and predicate(value, key, parent) then
+			if parent and key then parent[key] = modifier(value) end
+		end
+	end)
+end

processor/meta.go

@@ -0,0 +1,29 @@
+package processor
+
+import (
+	_ "embed"
+	"fmt"
+	"os"
+
+	logger "git.site.quack-lab.dev/dave/cylogger"
+)
+
+//go:embed meta.lua
+var metaFileContent string
+
+var metaLogger = logger.Default.WithPrefix("meta")
+
+// GenerateMetaFile generates meta.lua with function signatures for LuaLS autocomplete
+func GenerateMetaFile(outputPath string) error {
+	metaLogger.Info("Generating meta.lua file for LuaLS autocomplete")
+
+	// Write the embedded meta file
+	err := os.WriteFile(outputPath, []byte(metaFileContent), 0644)
+	if err != nil {
+		metaLogger.Error("Failed to write meta.lua: %v", err)
+		return fmt.Errorf("failed to write meta.lua: %w", err)
+	}
+
+	metaLogger.Info("Successfully generated meta.lua at %q", outputPath)
+	return nil
+}

processor/meta.lua

@@ -0,0 +1,245 @@
+---@meta
+
+---@class ParserOptions
+---@field delimiter string? The field delimiter (default: ",").
+---@field hasheader boolean? If true, first non-comment row is treated as headers (default: false).
+---@field hascomments boolean? If true, lines starting with '#' are skipped (default: false).
+
+---@class XMLElement
+---@field _tag string The XML tag name
+---@field _attr {[string]: string}? XML attributes as key-value pairs
+---@field _text string? Text content of the element
+---@field _children XMLElement[]? Child elements
+
+---@class JSONNode
+---@field [string] string | number | boolean | nil | JSONNode | JSONArray JSON object fields
+---@alias JSONArray (string | number | boolean | nil | JSONNode)[]
+
+---@class CSVRow
+---@field [integer] string Numeric indices for field access
+---@field Headers string[]? Header row if hasheader was true
+
+--- Returns the minimum of two numbers
+---@param a number First number
+---@param b number Second number
+---@return number #Minimum value
+function min(a, b) end
+
+--- Returns the maximum of two numbers
+---@param a number First number
+---@param b number Second number
+---@return number #Maximum value
+function max(a, b) end
+
+--- Rounds a number to n decimal places
+---@param x number Number to round
+---@param n number? Number of decimal places (default: 0)
+---@return number #Rounded number
+function round(x, n) end
+
+--- Returns the floor of a number
+---@param x number Number to floor
+---@return number #Floored number
+function floor(x) end
+
+--- Returns the ceiling of a number
+---@param x number Number to ceil
+---@return number #Ceiled number
+function ceil(x) end
+
+--- Converts string to uppercase
+---@param s string String to convert
+---@return string #Uppercase string
+function upper(s) end
+
+--- Converts string to lowercase
+---@param s string String to convert
+---@return string #Lowercase string
+function lower(s) end
+
+--- Formats a string using Lua string.format
+---@param s string Format string
+---@param ... any Values to format
+---@return string #Formatted string
+function format(s, ...) end
+
+--- Removes leading and trailing whitespace from string
+---@param s string String to trim
+---@return string #Trimmed string
+function trim(s) end
+
+--- Splits a string by separator
+---@param inputstr string String to split
+---@param sep string? Separator pattern (default: whitespace)
+---@return string[] #Array of string parts
+function strsplit(inputstr, sep) end
+
+--- Prints table structure recursively
+---@param table {[any]: any} Table to dump
+---@param depth number? Current depth (default: 0)
+function dump(table, depth) end
+
+--- Validates options against a set of valid option keys.
+---@param options ParserOptions? The options table to validate
+function areOptionsValid(options) end
+
+--- Parses CSV text into rows and fields using a minimal RFC 4180 state machine.
+--- Requirements/assumptions:<br>
+---   Input is a single string containing the entire CSV content.<br>
+---   Field separators are specified by delimiter option (default: comma).<br>
+---   Newlines between rows may be "\n" or "\r\n". "\r\n" is treated as one line break.<br>
+---   Fields may be quoted with double quotes (").<br>
+---   Inside quoted fields, doubled quotes ("") represent a literal quote character.<br>
+---   No backslash escaping is supported (not part of RFC 4180).<br>
+---   Newlines inside quoted fields are preserved as part of the field.<br>
+---   Leading/trailing spaces are preserved; no trimming is performed.<br>
+---   Empty fields and empty rows are preserved.<br>
+---   The final row is emitted even if the text does not end with a newline.<br>
+---   Lines starting with '#' (after optional leading whitespace) are treated as comments and skipped if hascomments is true.<br>
+---@param csv string The CSV text to parse.
+---@param options ParserOptions? Options for the parser
+---@return CSVRow[] #A table (array) of rows; each row is a table with numeric indices and optionally header-named keys.
+function fromCSV(csv, options) end
+
+--- Converts a table of rows back to CSV text format (RFC 4180 compliant).<br>
+--- Requirements:<br>
+---   Input is a table (array) of rows, where each row is a table (array) of field values.<br>
+---   Field values are converted to strings using tostring().<br>
+---   Fields are quoted if they contain the delimiter, newlines, or double quotes.<br>
+---   Double quotes inside quoted fields are doubled ("").<br>
+---   Fields are joined with the specified delimiter; rows are joined with newlines.<br>
+---   If includeHeaders is true and rows have a Headers field, headers are included as the first row.<br>
+---@param rows CSVRow[] Array of rows, where each row is an array of field values.
+---@param options ParserOptions? Options for the parser
+---@return string #CSV-formatted text
+function toCSV(rows, options) end
+
+--- Converts string to number, returns 0 if invalid
+---@param str string String to convert
+---@return number #Numeric value or 0
+function num(str) end
+
+--- Converts number to string
+---@param num number Number to convert
+---@return string #String representation
+function str(num) end
+
+--- Checks if string is numeric
+---@param str string String to check
+---@return boolean #True if string is numeric
+function is_number(str) end
+
+--- Checks if table is a sequential array (1-indexed with no gaps)
+---@param t {[integer]: any} Table to check
+---@return boolean #True if table is an array
+function isArray(t) end
+
+--- Find all elements with a specific tag name (recursive search)
+---@param root XMLElement The root XML element (with _tag, _attr, _children fields)
+---@param tagName string The tag name to search for
+---@return XMLElement[] #Array of matching elements
+function findElements(root, tagName) end
+
+--- Visit all elements recursively and call a function on each
+---@param root XMLElement The root XML element
+---@param callback fun(element: XMLElement, depth: number, path: string) Function to call with each element
+function visitElements(root, callback) end
+
+--- Get numeric value from XML element attribute
+---@param element XMLElement XML element with _attr field
+---@param attrName string Attribute name
+---@return number? #The numeric value or nil if not found/not numeric
+function getNumAttr(element, attrName) end
+
+--- Set numeric value to XML element attribute
+---@param element XMLElement XML element with _attr field
+---@param attrName string Attribute name
+---@param value number Numeric value to set
+function setNumAttr(element, attrName, value) end
+
+--- Modify numeric attribute by applying a function
+---@param element XMLElement XML element
+---@param attrName string Attribute name
+---@param func fun(currentValue: number): number Function that takes current value and returns new value
+---@return boolean #True if modification was made
+function modifyNumAttr(element, attrName, func) end
+
+--- Find all elements matching a predicate function
+---@param root XMLElement The root XML element
+---@param predicate fun(element: XMLElement): boolean Function that takes element and returns true/false
+---@return XMLElement[] #Array of matching elements
+function filterElements(root, predicate) end
+
+--- Get text content of an element
+---@param element XMLElement XML element
+---@return string? #The text content or nil
+function getText(element) end
+
+--- Set text content of an element
+---@param element XMLElement XML element
+---@param text string Text content to set
+function setText(element, text) end
+
+--- Check if element has an attribute
+---@param element XMLElement XML element
+---@param attrName string Attribute name
+---@return boolean #True if attribute exists
+function hasAttr(element, attrName) end
+
+--- Get attribute value as string
+---@param element XMLElement XML element
+---@param attrName string Attribute name
+---@return string? #The attribute value or nil
+function getAttr(element, attrName) end
+
+--- Set attribute value
+---@param element XMLElement XML element
+---@param attrName string Attribute name
+---@param value string | number | boolean Value to set (will be converted to string)
+function setAttr(element, attrName, value) end
+
+--- Find first element with a specific tag name (searches direct children only)
+---@param parent XMLElement The parent XML element
+---@param tagName string The tag name to search for
+---@return XMLElement? #The first matching element or nil
+function findFirstElement(parent, tagName) end
+
+--- Add a child element to a parent
+---@param parent XMLElement The parent XML element
+---@param child XMLElement The child element to add
+function addChild(parent, child) end
+
+--- Remove all children with a specific tag name
+---@param parent XMLElement The parent XML element
+---@param tagName string The tag name to remove
+---@return number #Count of removed children
+function removeChildren(parent, tagName) end
+
+--- Get all direct children with a specific tag name
+---@param parent XMLElement The parent XML element
+---@param tagName string The tag name to search for
+---@return XMLElement[] #Array of matching children
+function getChildren(parent, tagName) end
+
+--- Count children with a specific tag name
+---@param parent XMLElement The parent XML element
+---@param tagName string The tag name to count
+---@return number #Count of matching children
+function countChildren(parent, tagName) end
+
+--- Recursively visit all values in a JSON structure
+---@param data JSONNode | JSONArray JSON data (nested tables)
+---@param callback fun(value: string | number | boolean | nil | JSONNode | JSONArray, key: string?, parent: JSONNode?): nil Function called with (value, key, parent)
+function visitJSON(data, callback) end
+
+--- Find all values in JSON matching a predicate
+---@param data JSONNode | JSONArray JSON data
+---@param predicate fun(value: string | number | boolean | nil | JSONNode | JSONArray, key: string?, parent: JSONNode?): boolean Function that takes (value, key, parent) and returns true/false
+---@return (string | number | boolean | nil | JSONNode | JSONArray)[] #Array of matching values
+function findInJSON(data, predicate) end
+
+--- Modify all numeric values in JSON matching a condition
+---@param data JSONNode | JSONArray JSON data
+---@param predicate fun(value: string | number | boolean | nil | JSONNode | JSONArray, key: string?, parent: JSONNode?): boolean Function that takes (value, key, parent) and returns true/false
+---@param modifier fun(currentValue: number): number Function that takes current value and returns new value
+function modifyJSONNumbers(data, predicate, modifier) end

processor/processor.go

@@ -1,155 +1,154 @@
 package processor
 
 import (
+	_ "embed"
 	"fmt"
+	"io"
+	"net/http"
+	"os"
+	"path/filepath"
+	"regexp"
 	"strings"
 
-	lua "github.com/yuin/gopher-lua"
+	"cook/utils"
 
-	"modify/logger"
+	logger "git.site.quack-lab.dev/dave/cylogger"
+	lua "github.com/yuin/gopher-lua"
 )
 
+//go:embed luahelper.lua
+var helperScript string
+
+// processorLogger is a scoped logger for the processor package.
+var processorLogger = logger.Default.WithPrefix("processor")
+
 // Maybe we make this an interface again for the shits and giggles
 // We will see, it could easily be...
 
+var globalVariables = map[string]interface{}{}
+
+func SetVariables(vars map[string]interface{}) {
+	for k, v := range vars {
+		globalVariables[k] = v
+	}
+}
+
 func NewLuaState() (*lua.LState, error) {
+	newLStateLogger := processorLogger.WithPrefix("NewLuaState")
+	newLStateLogger.Debug("Creating new Lua state")
 	L := lua.NewState()
 	// defer L.Close()
 
 	// Load math library
-	logger.Debug("Loading Lua math library")
+	newLStateLogger.Debug("Loading Lua math library")
 	L.Push(L.GetGlobal("require"))
 	L.Push(lua.LString("math"))
 	if err := L.PCall(1, 1, nil); err != nil {
-		logger.Error("Failed to load Lua math library: %v", err)
+		newLStateLogger.Error("Failed to load Lua math library: %v", err)
 		return nil, fmt.Errorf("error loading Lua math library: %v", err)
 	}
+	newLStateLogger.Debug("Lua math library loaded")
 
 	// Initialize helper functions
-	logger.Debug("Initializing Lua helper functions")
+	newLStateLogger.Debug("Initializing Lua helper functions")
 	if err := InitLuaHelpers(L); err != nil {
-		logger.Error("Failed to initialize Lua helper functions: %v", err)
+		newLStateLogger.Error("Failed to initialize Lua helper functions: %v", err)
 		return nil, err
 	}
+	newLStateLogger.Debug("Lua helper functions initialized")
 
+	// Inject global variables
+	if len(globalVariables) > 0 {
+		newLStateLogger.Debug("Injecting %d global variables into Lua state", len(globalVariables))
+		for k, v := range globalVariables {
+			switch val := v.(type) {
+			case int:
+				L.SetGlobal(k, lua.LNumber(float64(val)))
+			case int64:
+				L.SetGlobal(k, lua.LNumber(float64(val)))
+			case float32:
+				L.SetGlobal(k, lua.LNumber(float64(val)))
+			case float64:
+				L.SetGlobal(k, lua.LNumber(val))
+			case string:
+				L.SetGlobal(k, lua.LString(val))
+			case bool:
+				if val {
+					L.SetGlobal(k, lua.LTrue)
+				} else {
+					L.SetGlobal(k, lua.LFalse)
+				}
+			default:
+				// Fallback to string representation
+				L.SetGlobal(k, lua.LString(fmt.Sprintf("%v", val)))
+			}
+		}
+	}
+
+	newLStateLogger.Debug("New Lua state created successfully")
 	return L, nil
 }
 
-// func Process(filename string, pattern string, luaExpr string) (int, int, error) {
-// 	logger.Debug("Processing file %q with pattern %q", filename, pattern)
-//
-// 	// Read file content
-// 	cwd, err := os.Getwd()
-// 	if err != nil {
-// 		logger.Error("Failed to get current working directory: %v", err)
-// 		return 0, 0, fmt.Errorf("error getting current working directory: %v", err)
-// 	}
-//
-// 	fullPath := filepath.Join(cwd, filename)
-// 	logger.Trace("Reading file from: %s", fullPath)
-//
-// 	stat, err := os.Stat(fullPath)
-// 	if err != nil {
-// 		logger.Error("Failed to stat file %s: %v", fullPath, err)
-// 		return 0, 0, fmt.Errorf("error getting file info: %v", err)
-// 	}
-// 	logger.Debug("File size: %d bytes, modified: %s", stat.Size(), stat.ModTime().Format(time.RFC3339))
-//
-// 	content, err := os.ReadFile(fullPath)
-// 	if err != nil {
-// 		logger.Error("Failed to read file %s: %v", fullPath, err)
-// 		return 0, 0, fmt.Errorf("error reading file: %v", err)
-// 	}
-//
-// 	fileContent := string(content)
-// 	logger.Trace("File read successfully: %d bytes, hash: %x", len(content), md5sum(content))
-//
-// 	// Detect and log file type
-// 	fileType := detectFileType(filename, fileContent)
-// 	if fileType != "" {
-// 		logger.Debug("Detected file type: %s", fileType)
-// 	}
-//
-// 	// Process the content
-// 	logger.Debug("Starting content processing")
-// 	modifiedContent, modCount, matchCount, err := ProcessContent(fileContent, pattern, luaExpr)
-// 	if err != nil {
-// 		logger.Error("Processing error: %v", err)
-// 		return 0, 0, err
-// 	}
-//
-// 	logger.Debug("Processing results: %d matches, %d modifications", matchCount, modCount)
-//
-// 	// If we made modifications, save the file
-// 	if modCount > 0 {
-// 		// Calculate changes summary
-// 		changePercent := float64(len(modifiedContent)) / float64(len(fileContent)) * 100
-// 		logger.Info("File size change: %d → %d bytes (%.1f%%)",
-// 			len(fileContent), len(modifiedContent), changePercent)
-//
-// 		logger.Debug("Writing modified content to %s", fullPath)
-// 		err = os.WriteFile(fullPath, []byte(modifiedContent), 0644)
-// 		if err != nil {
-// 			logger.Error("Failed to write to file %s: %v", fullPath, err)
-// 			return 0, 0, fmt.Errorf("error writing file: %v", err)
-// 		}
-// 		logger.Debug("File written successfully, new hash: %x", md5sum([]byte(modifiedContent)))
-// 	} else if matchCount > 0 {
-// 		logger.Debug("No content modifications needed for %d matches", matchCount)
-// 	} else {
-// 		logger.Debug("No matches found in file")
-// 	}
-//
-// 	return modCount, matchCount, nil
-// }
-
 // FromLua converts a Lua table to a struct or map recursively
 func FromLua(L *lua.LState, luaValue lua.LValue) (interface{}, error) {
+	fromLuaLogger := processorLogger.WithPrefix("FromLua").WithField("luaType", luaValue.Type().String())
+	fromLuaLogger.Debug("Converting Lua value to Go interface")
 	switch v := luaValue.(type) {
-	// Well shit...
-	// Tables in lua are both maps and arrays
-	// As arrays they are ordered and as maps, obviously, not
-	// So when we parse them to a go map we fuck up the order for arrays
-	// We have to find a better way....
 	case *lua.LTable:
+		fromLuaLogger.Debug("Processing Lua table")
 		isArray, err := IsLuaTableArray(L, v)
 		if err != nil {
+			fromLuaLogger.Error("Failed to determine if Lua table is array: %v", err)
 			return nil, err
 		}
+		fromLuaLogger.Debug("Lua table is array: %t", isArray)
 		if isArray {
+			fromLuaLogger.Debug("Converting Lua table to Go array")
 			result := make([]interface{}, 0)
 			v.ForEach(func(key lua.LValue, value lua.LValue) {
 				converted, _ := FromLua(L, value)
 				result = append(result, converted)
 			})
+			fromLuaLogger.Trace("Converted Go array: %v", result)
 			return result, nil
 		} else {
+			fromLuaLogger.Debug("Converting Lua table to Go map")
 			result := make(map[string]interface{})
 			v.ForEach(func(key lua.LValue, value lua.LValue) {
 				converted, _ := FromLua(L, value)
 				result[key.String()] = converted
 			})
+			fromLuaLogger.Trace("Converted Go map: %v", result)
 			return result, nil
 		}
 	case lua.LString:
+		fromLuaLogger.Debug("Converting Lua string to Go string")
+		fromLuaLogger.Trace("Lua string: %q", string(v))
 		return string(v), nil
 	case lua.LBool:
+		fromLuaLogger.Debug("Converting Lua boolean to Go boolean")
+		fromLuaLogger.Trace("Lua boolean: %t", bool(v))
 		return bool(v), nil
 	case lua.LNumber:
+		fromLuaLogger.Debug("Converting Lua number to Go float64")
+		fromLuaLogger.Trace("Lua number: %f", float64(v))
 		return float64(v), nil
 	default:
+		fromLuaLogger.Debug("Unsupported Lua type, returning nil")
 		return nil, nil
 	}
 }
 
 func IsLuaTableArray(L *lua.LState, v *lua.LTable) (bool, error) {
-	logger.Trace("Checking if Lua table is an array")
+	isLuaTableArrayLogger := processorLogger.WithPrefix("IsLuaTableArray")
+	isLuaTableArrayLogger.Debug("Checking if Lua table is an array")
+	isLuaTableArrayLogger.Trace("Lua table input: %v", v)
 	L.SetGlobal("table_to_check", v)
 
 	// Use our predefined helper function from InitLuaHelpers
 	err := L.DoString(`is_array = isArray(table_to_check)`)
 	if err != nil {
-		logger.Error("Error determining if table is an array: %v", err)
+		isLuaTableArrayLogger.Error("Error determining if table is an array: %v", err)
 		return false, fmt.Errorf("error determining if table is array: %w", err)
 	}
 
@@ -157,111 +156,33 @@ func IsLuaTableArray(L *lua.LState, v *lua.LTable) (bool, error) {
 	isArray := L.GetGlobal("is_array")
 	// LVIsFalse returns true if a given LValue is a nil or false otherwise false.
 	result := !lua.LVIsFalse(isArray)
-	logger.Trace("Lua table is array: %v", result)
+	isLuaTableArrayLogger.Debug("Lua table is array: %t", result)
+	isLuaTableArrayLogger.Trace("isArray result Lua value: %v", isArray)
 	return result, nil
 }
 
 // InitLuaHelpers initializes common Lua helper functions
 func InitLuaHelpers(L *lua.LState) error {
-	logger.Debug("Loading Lua helper functions")
+	initLuaHelpersLogger := processorLogger.WithPrefix("InitLuaHelpers")
+	initLuaHelpersLogger.Debug("Loading Lua helper functions")
 
-	helperScript := `
--- Custom Lua helpers for math operations
-function min(a, b) return math.min(a, b) end
-function max(a, b) return math.max(a, b) end
-function round(x, n)
-	if n == nil then n = 0 end
-	return math.floor(x * 10^n + 0.5) / 10^n
-end
-function floor(x) return math.floor(x) end
-function ceil(x) return math.ceil(x) end
-function upper(s) return string.upper(s) end
-function lower(s) return string.lower(s) end
-function format(s, ...) return string.format(s, ...) end
-
--- String split helper
-function strsplit(inputstr, sep)
-  if sep == nil then
-    sep = "%s"
-  end
-  local t = {}
-  for str in string.gmatch(inputstr, "([^"..sep.."]+)") do
-    table.insert(t, str)
-  end
-  return t
-end
-
----@param table table
----@param depth number?
-function DumpTable(table, depth)
-	if depth == nil then
-		depth = 0
-	end
-	if (depth > 200) then
-		print("Error: Depth > 200 in dumpTable()")
-		return
-	end
-	for k, v in pairs(table) do
-		if (type(v) == "table") then
-			print(string.rep("  ", depth) .. k .. ":")
-			DumpTable(v, depth + 1)
-		else
-			print(string.rep("  ", depth) .. k .. ": ", v)
-		end
-	end
-end
-
--- String to number conversion helper
-function num(str)
-    return tonumber(str) or 0
-end
-
--- Number to string conversion
-function str(num)
-    return tostring(num)
-end
-
--- Check if string is numeric
-function is_number(str)
-    return tonumber(str) ~= nil
-end
-
-function isArray(t)
-    if type(t) ~= "table" then return false end
-    local max = 0
-    local count = 0
-    for k, _ in pairs(t) do
-        if type(k) ~= "number" or k < 1 or math.floor(k) ~= k then
-            return false
-        end
-        max = math.max(max, k)
-        count = count + 1
-    end
-    return max == count
-end
-
-modified = false
-`
 	if err := L.DoString(helperScript); err != nil {
-		logger.Error("Failed to load Lua helper functions: %v", err)
+		initLuaHelpersLogger.Error("Failed to load Lua helper functions: %v", err)
 		return fmt.Errorf("error loading helper functions: %v", err)
 	}
+	initLuaHelpersLogger.Debug("Lua helper functions loaded")
 
-	logger.Debug("Setting up Lua print function to Go")
+	initLuaHelpersLogger.Debug("Setting up Lua print function to Go")
 	L.SetGlobal("print", L.NewFunction(printToGo))
+	L.SetGlobal("fetch", L.NewFunction(fetch))
+	L.SetGlobal("re", L.NewFunction(EvalRegex))
+	initLuaHelpersLogger.Debug("Lua print and fetch functions bound to Go")
 	return nil
 }
 
-// LimitString truncates a string to maxLen and adds "..." if truncated
-func LimitString(s string, maxLen int) string {
-	s = strings.ReplaceAll(s, "\n", "\\n")
-	if len(s) <= maxLen {
-		return s
-	}
-	return s[:maxLen-3] + "..."
-}
-
 func PrependLuaAssignment(luaExpr string) string {
+	prependLuaAssignmentLogger := processorLogger.WithPrefix("PrependLuaAssignment").WithField("originalLuaExpr", luaExpr)
+	prependLuaAssignmentLogger.Debug("Prepending Lua assignment if necessary")
 	// Auto-prepend v1 for expressions starting with operators
 	if strings.HasPrefix(luaExpr, "*") ||
 		strings.HasPrefix(luaExpr, "/") ||
@@ -270,30 +191,83 @@ func PrependLuaAssignment(luaExpr string) string {
 		strings.HasPrefix(luaExpr, "^") ||
 		strings.HasPrefix(luaExpr, "%") {
 		luaExpr = "v1 = v1" + luaExpr
+		prependLuaAssignmentLogger.Debug("Prepended 'v1 = v1' due to operator prefix")
 	} else if strings.HasPrefix(luaExpr, "=") {
 		// Handle direct assignment with = operator
 		luaExpr = "v1 " + luaExpr
+		prependLuaAssignmentLogger.Debug("Prepended 'v1' due to direct assignment operator")
 	}
 
 	// Add assignment if needed
 	if !strings.Contains(luaExpr, "=") {
 		luaExpr = "v1 = " + luaExpr
+		prependLuaAssignmentLogger.Debug("Prepended 'v1 =' as no assignment was found")
 	}
+	prependLuaAssignmentLogger.Trace("Final Lua expression after prepending: %q", luaExpr)
 	return luaExpr
 }
 
+// LoadExternalLuaFile loads Lua code from an external file
+func LoadExternalLuaFile(luaPath string, sourceDir string) (string, error) {
+	loadLuaLogger := processorLogger.WithPrefix("LoadExternalLuaFile").WithField("luaPath", luaPath).WithField("sourceDir", sourceDir)
+	loadLuaLogger.Debug("Loading external Lua file")
+
+	// Resolve path: if relative, resolve relative to sourceDir; if absolute, use as-is
+	var resolvedPath string
+	if filepath.IsAbs(luaPath) {
+		resolvedPath = luaPath
+	} else {
+		if sourceDir == "" {
+			// No source directory, use current working directory
+			cwd, err := os.Getwd()
+			if err != nil {
+				loadLuaLogger.Error("Failed to get current working directory: %v", err)
+				return "", fmt.Errorf("failed to get current working directory: %w", err)
+			}
+			resolvedPath = filepath.Join(cwd, luaPath)
+		} else {
+			resolvedPath = filepath.Join(sourceDir, luaPath)
+		}
+	}
+
+	// Normalize path
+	resolvedPath = filepath.Clean(resolvedPath)
+	loadLuaLogger.Debug("Resolved Lua file path: %q", resolvedPath)
+
+	// Read the file
+	content, err := os.ReadFile(resolvedPath)
+	if err != nil {
+		loadLuaLogger.Error("Failed to read Lua file %q: %v", resolvedPath, err)
+		return "", fmt.Errorf("failed to read Lua file %q: %w", luaPath, err)
+	}
+
+	loadLuaLogger.Debug("Successfully loaded %d bytes from Lua file %q", len(content), resolvedPath)
+	return string(content), nil
+}
+
 // BuildLuaScript prepares a Lua expression from shorthand notation
-func BuildLuaScript(luaExpr string) string {
-	logger.Debug("Building Lua script from expression: %s", luaExpr)
+func BuildLuaScript(luaExpr string, sourceDir string) string {
+	buildLuaScriptLogger := processorLogger.WithPrefix("BuildLuaScript").WithField("inputLuaExpr", luaExpr)
+	buildLuaScriptLogger.Debug("Building full Lua script from expression")
+
+	// Check if this is an external Lua file reference
+	if strings.HasPrefix(luaExpr, "@") {
+		luaPath := strings.TrimPrefix(luaExpr, "@")
+		externalLua, err := LoadExternalLuaFile(luaPath, sourceDir)
+		if err != nil {
+			buildLuaScriptLogger.Error("Failed to load external Lua file: %v", err)
+			// Return error script that will fail at runtime
+			return fmt.Sprintf(`error("Failed to load external Lua file: %v")`, err)
+		}
+		luaExpr = externalLua
+		buildLuaScriptLogger.Debug("Loaded external Lua file, %d characters", len(luaExpr))
+	}
+
+	// Perform $var substitutions from globalVariables
+	luaExpr = replaceVariables(luaExpr)
 
 	luaExpr = PrependLuaAssignment(luaExpr)
 
-	// This allows the user to specify whether or not they modified a value
-	// If they do nothing we assume they did modify (no return at all)
-	// If they return before our return then they themselves specify what they did
-	// If nothing is returned lua assumes nil
-	// So we can say our value was modified if the return value is either nil or true
-	// If the return value is false then the user wants to keep the original
 	fullScript := fmt.Sprintf(`
 		function run()
 			%s
@@ -301,11 +275,73 @@ func BuildLuaScript(luaExpr string) string {
 		local res = run()
 		modified = res == nil or res
 	`, luaExpr)
+	buildLuaScriptLogger.Trace("Generated full Lua script: %q", utils.LimitString(fullScript, 200))
 
 	return fullScript
 }
 
+// BuildJSONLuaScript prepares a Lua expression for JSON mode
+func BuildJSONLuaScript(luaExpr string, sourceDir string) string {
+	buildJSONLuaScriptLogger := processorLogger.WithPrefix("BuildJSONLuaScript").WithField("inputLuaExpr", luaExpr)
+	buildJSONLuaScriptLogger.Debug("Building full Lua script for JSON mode from expression")
+
+	// Check if this is an external Lua file reference
+	if strings.HasPrefix(luaExpr, "@") {
+		luaPath := strings.TrimPrefix(luaExpr, "@")
+		externalLua, err := LoadExternalLuaFile(luaPath, sourceDir)
+		if err != nil {
+			buildJSONLuaScriptLogger.Error("Failed to load external Lua file: %v", err)
+			// Return error script that will fail at runtime
+			return fmt.Sprintf(`error("Failed to load external Lua file: %v")`, err)
+		}
+		luaExpr = externalLua
+		buildJSONLuaScriptLogger.Debug("Loaded external Lua file, %d characters", len(luaExpr))
+	}
+
+	// Perform $var substitutions from globalVariables
+	luaExpr = replaceVariables(luaExpr)
+
+	fullScript := fmt.Sprintf(`
+		function run()
+			%s
+		end
+		local res = run()
+		modified = res == nil or res
+	`, luaExpr)
+	buildJSONLuaScriptLogger.Trace("Generated full JSON Lua script: %q", utils.LimitString(fullScript, 200))
+
+	return fullScript
+}
+
+func replaceVariables(expr string) string {
+	// $varName -> literal value
+	varNameRe := regexp.MustCompile(`\$(\w+)`)
+	return varNameRe.ReplaceAllStringFunc(expr, func(m string) string {
+		name := varNameRe.FindStringSubmatch(m)[1]
+		if v, ok := globalVariables[name]; ok {
+			switch val := v.(type) {
+			case int, int64, float32, float64:
+				return fmt.Sprintf("%v", val)
+			case bool:
+				if val {
+					return "true"
+				} else {
+					return "false"
+				}
+			case string:
+				// Quote strings for Lua literal
+				return fmt.Sprintf("%q", val)
+			default:
+				return fmt.Sprintf("%q", fmt.Sprintf("%v", val))
+			}
+		}
+		return m
+	})
+}
+
 func printToGo(L *lua.LState) int {
+	printToGoLogger := processorLogger.WithPrefix("printToGo")
+	printToGoLogger.Debug("Lua print function called, redirecting to Go logger")
 	top := L.GetTop()
 
 	args := make([]interface{}, top)
@@ -319,8 +355,254 @@ func printToGo(L *lua.LState) int {
 		parts = append(parts, fmt.Sprintf("%v", arg))
 	}
 	message := strings.Join(parts, " ")
+	printToGoLogger.Trace("Lua print message: %q", message)
 
 	// Use the LUA log level with a script tag
 	logger.Lua("%s", message)
+	printToGoLogger.Debug("Message logged from Lua")
 	return 0
 }
+
+func fetch(L *lua.LState) int {
+	fetchLogger := processorLogger.WithPrefix("fetch")
+	fetchLogger.Debug("Lua fetch function called")
+	// Get URL from first argument
+	url := L.ToString(1)
+	if url == "" {
+		fetchLogger.Error("Fetch failed: URL is required")
+		L.Push(lua.LNil)
+		L.Push(lua.LString("URL is required"))
+		return 2
+	}
+	fetchLogger.Debug("Fetching URL: %q", url)
+
+	// Get options from second argument if provided
+	var method = "GET"
+	var headers = make(map[string]string)
+	var body = ""
+
+	if L.GetTop() > 1 {
+		options := L.ToTable(2)
+		if options != nil {
+			fetchLogger.Debug("Processing fetch options")
+			// Get method
+			if methodVal := options.RawGetString("method"); methodVal != lua.LNil {
+				method = methodVal.String()
+				fetchLogger.Trace("Method from options: %q", method)
+			}
+
+			// Get headers
+			if headersVal := options.RawGetString("headers"); headersVal != lua.LNil {
+				if headersTable, ok := headersVal.(*lua.LTable); ok {
+					fetchLogger.Trace("Processing headers table")
+					headersTable.ForEach(func(key lua.LValue, value lua.LValue) {
+						headers[key.String()] = value.String()
+						fetchLogger.Trace("Header: %q = %q", key.String(), value.String())
+					})
+				}
+				fetchLogger.Trace("All headers: %v", headers)
+			}
+
+			// Get body
+			if bodyVal := options.RawGetString("body"); bodyVal != lua.LNil {
+				body = bodyVal.String()
+				fetchLogger.Trace("Body from options: %q", utils.LimitString(body, 100))
+			}
+		}
+	}
+	fetchLogger.Debug("Fetch request details: Method=%q, URL=%q, BodyLength=%d, Headers=%v", method, url, len(body), headers)
+
+	// Create HTTP request
+	req, err := http.NewRequest(method, url, strings.NewReader(body))
+	if err != nil {
+		fetchLogger.Error("Error creating HTTP request: %v", err)
+		L.Push(lua.LNil)
+		L.Push(lua.LString(fmt.Sprintf("Error creating request: %v", err)))
+		return 2
+	}
+
+	// Set headers
+	for key, value := range headers {
+		req.Header.Set(key, value)
+	}
+	fetchLogger.Debug("HTTP request created and headers set")
+	fetchLogger.Trace("HTTP Request: %+v", req)
+
+	// Make request
+	client := &http.Client{}
+	resp, err := client.Do(req)
+	if err != nil {
+		fetchLogger.Error("Error making HTTP request: %v", err)
+		L.Push(lua.LNil)
+		L.Push(lua.LString(fmt.Sprintf("Error making request: %v", err)))
+		return 2
+	}
+	defer func() {
+		fetchLogger.Debug("Closing HTTP response body")
+		resp.Body.Close()
+	}()
+	fetchLogger.Debug("HTTP request executed. Status Code: %d", resp.StatusCode)
+
+	// Read response body
+	bodyBytes, err := io.ReadAll(resp.Body)
+	if err != nil {
+		fetchLogger.Error("Error reading response body: %v", err)
+		L.Push(lua.LNil)
+		L.Push(lua.LString(fmt.Sprintf("Error reading response: %v", err)))
+		return 2
+	}
+	fetchLogger.Trace("Response body length: %d", len(bodyBytes))
+
+	// Create response table
+	responseTable := L.NewTable()
+	responseTable.RawSetString("status", lua.LNumber(resp.StatusCode))
+	responseTable.RawSetString("statusText", lua.LString(resp.Status))
+	responseTable.RawSetString("ok", lua.LBool(resp.StatusCode >= 200 && resp.StatusCode < 300))
+	responseTable.RawSetString("body", lua.LString(string(bodyBytes)))
+	fetchLogger.Debug("Created Lua response table")
+
+	// Set headers in response
+	headersTable := L.NewTable()
+	for key, values := range resp.Header {
+		headersTable.RawSetString(key, lua.LString(values[0]))
+		fetchLogger.Trace("Response header: %q = %q", key, values[0])
+	}
+	responseTable.RawSetString("headers", headersTable)
+	fetchLogger.Trace("Full response table: %v", responseTable)
+
+	L.Push(responseTable)
+	fetchLogger.Debug("Pushed response table to Lua stack")
+	return 1
+}
+
+func EvalRegex(L *lua.LState) int {
+	evalRegexLogger := processorLogger.WithPrefix("evalRegex")
+	evalRegexLogger.Debug("Lua evalRegex function called")
+
+	pattern := L.ToString(1)
+	input := L.ToString(2)
+
+	evalRegexLogger.Debug("Pattern: %q, Input: %q", pattern, input)
+
+	re := regexp.MustCompile(pattern)
+	matches := re.FindStringSubmatch(input)
+
+	evalRegexLogger.Debug("Go regex matches: %v (count: %d)", matches, len(matches))
+	evalRegexLogger.Debug("Matches is nil: %t", matches == nil)
+
+	if len(matches) > 0 {
+		matchesTable := L.NewTable()
+		for i, match := range matches {
+			matchesTable.RawSetInt(i+1, lua.LString(match))
+			evalRegexLogger.Debug("Set table[%d] = %q", i+1, match)
+		}
+		L.Push(matchesTable)
+	} else {
+		L.Push(lua.LNil)
+	}
+
+	evalRegexLogger.Debug("Pushed matches table to Lua stack")
+
+	return 1
+}
+
+// GetLuaFunctionsHelp returns a comprehensive help string for all available Lua functions
+func GetLuaFunctionsHelp() string {
+	return `Lua Functions Available in Global Environment:
+
+MATH FUNCTIONS:
+  min(a, b)   - Returns the minimum of two numbers
+  max(a, b)   - Returns the maximum of two numbers
+  round(x, n) - Rounds x to n decimal places (default 0)
+  floor(x)    - Returns the floor of x
+  ceil(x)     - Returns the ceiling of x
+
+STRING FUNCTIONS:
+  upper(s)                - Converts string to uppercase
+  lower(s)                - Converts string to lowercase
+  format(s, ...)          - Formats string using Lua string.format
+  trim(s)                 - Removes leading/trailing whitespace
+  strsplit(inputstr, sep) - Splits string by separator (default: whitespace)
+  fromCSV(csv, options)   - Parses CSV text into rows of fields
+    options: {delimiter=",", hasheader=false, hascomments=false}
+  toCSV(rows, options)    - Converts table of rows to CSV text format
+    options: {delimiter=",", hasheader=false}
+  num(str)                - Converts string to number (returns 0 if invalid)
+  str(num)                - Converts number to string
+  is_number(str)          - Returns true if string is numeric
+
+TABLE FUNCTIONS:
+  dump(table, depth) - Prints table structure recursively
+  isArray(t)         - Returns true if table is a sequential array
+
+XML HELPER FUNCTIONS:
+  findElements(root, tagName)           - Find all elements with specific tag name (recursive)
+  findFirstElement(parent, tagName)     - Find first direct child with specific tag name
+  visitElements(root, callback)         - Visit all elements recursively
+    callback(element, depth, path)
+  filterElements(root, predicate)       - Find elements matching condition
+    predicate(element) returns true/false
+  getNumAttr(element, attrName)         - Get numeric attribute value
+  setNumAttr(element, attrName, value)  - Set numeric attribute value
+  modifyNumAttr(element, attrName, func)- Modify numeric attribute with function
+    func(currentValue) returns newValue
+  hasAttr(element, attrName)            - Check if attribute exists
+  getAttr(element, attrName)            - Get attribute value as string
+  setAttr(element, attrName, value)     - Set attribute value
+  getText(element)                      - Get element text content
+  setText(element, text)                - Set element text content
+  addChild(parent, child)               - Add child element to parent
+  removeChildren(parent, tagName)       - Remove all children with specific tag name
+  getChildren(parent, tagName)          - Get all direct children with specific tag name
+  countChildren(parent, tagName)        - Count direct children with specific tag name
+
+JSON HELPER FUNCTIONS:
+  visitJSON(data, callback)                    - Visit all values in JSON structure
+    callback(value, key, parent)
+  findInJSON(data, predicate)                  - Find values matching condition
+    predicate(value, key, parent) returns true/false
+  modifyJSONNumbers(data, predicate, modifier) - Modify numeric values
+    predicate(value, key, parent) returns true/false
+    modifier(currentValue) returns newValue
+
+HTTP FUNCTIONS:
+  fetch(url, options) - Makes HTTP request, returns response table
+    options: {method="GET", headers={}, body=""}
+    returns: {status, statusText, ok, body, headers}
+
+REGEX FUNCTIONS:
+  re(pattern, input)  - Applies regex pattern to input string
+    returns: table with matches (index 0 = full match, 1+ = groups)
+
+UTILITY FUNCTIONS:
+  print(...)          - Prints arguments to Go logger
+
+EXAMPLES:
+  -- Math
+  round(3.14159, 2)      -> 3.14
+  min(5, 3)              -> 3
+  
+  -- String
+  strsplit("a,b,c", ",") -> {"a", "b", "c"}
+  upper("hello")         -> "HELLO"
+  num("123")             -> 123
+  
+  -- XML (where root is XML element with _tag, _attr, _children fields)
+  local items = findElements(root, "Item")
+  for _, item in ipairs(items) do
+    modifyNumAttr(item, "Weight", function(w) return w * 2 end)
+  end
+  
+  -- JSON (where data is parsed JSON object)
+  visitJSON(data, function(value, key, parent)
+    if type(value) == "number" and key == "price" then
+      parent[key] = value * 1.5
+    end
+  end)
+  
+  -- HTTP
+  local response = fetch("https://api.example.com/data")
+  if response.ok then
+    print(response.body)
+  end`
+}

processor/processor_coverage_test.go

@@ -0,0 +1,218 @@
+package processor
+
+import (
+	"net/http"
+	"net/http/httptest"
+	"testing"
+
+	"github.com/stretchr/testify/assert"
+	lua "github.com/yuin/gopher-lua"
+)
+
+// Test replaceVariables function
+func TestReplaceVariables(t *testing.T) {
+	// Setup global variables
+	globalVariables = map[string]interface{}{
+		"multiplier": 2.5,
+		"prefix":     "TEST_",
+		"enabled":    true,
+		"disabled":   false,
+		"count":      42,
+	}
+	defer func() {
+		globalVariables = make(map[string]interface{})
+	}()
+
+	tests := []struct {
+		name     string
+		input    string
+		expected string
+	}{
+		{
+			name:     "Replace numeric variable",
+			input:    "v1 * $multiplier",
+			expected: "v1 * 2.5",
+		},
+		{
+			name:     "Replace string variable",
+			input:    `s1 = $prefix .. "value"`,
+			expected: `s1 = "TEST_" .. "value"`,
+		},
+		{
+			name:     "Replace boolean true",
+			input:    "enabled = $enabled",
+			expected: "enabled = true",
+		},
+		{
+			name:     "Replace boolean false",
+			input:    "disabled = $disabled",
+			expected: "disabled = false",
+		},
+		{
+			name:     "Replace integer",
+			input:    "count = $count",
+			expected: "count = 42",
+		},
+		{
+			name:     "Multiple replacements",
+			input:    "$count * $multiplier",
+			expected: "42 * 2.5",
+		},
+		{
+			name:     "No variables",
+			input:    "v1 * 2",
+			expected: "v1 * 2",
+		},
+		{
+			name:     "Undefined variable",
+			input:    "v1 * $undefined",
+			expected: "v1 * $undefined",
+		},
+	}
+
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			result := replaceVariables(tt.input)
+			assert.Equal(t, tt.expected, result)
+		})
+	}
+}
+
+// Test SetVariables with all type cases
+func TestSetVariablesAllTypes(t *testing.T) {
+	vars := map[string]interface{}{
+		"int_val":     42,
+		"int64_val":   int64(100),
+		"float32_val": float32(3.14),
+		"float64_val": 2.718,
+		"bool_true":   true,
+		"bool_false":  false,
+		"string_val":  "hello",
+	}
+
+	SetVariables(vars)
+
+	// Create Lua state to verify
+	L, err := NewLuaState()
+	assert.NoError(t, err)
+	defer L.Close()
+
+	// Verify int64
+	int64Val := L.GetGlobal("int64_val")
+	assert.Equal(t, lua.LTNumber, int64Val.Type())
+	assert.Equal(t, 100.0, float64(int64Val.(lua.LNumber)))
+
+	// Verify float32
+	float32Val := L.GetGlobal("float32_val")
+	assert.Equal(t, lua.LTNumber, float32Val.Type())
+	assert.InDelta(t, 3.14, float64(float32Val.(lua.LNumber)), 0.01)
+
+	// Verify bool true
+	boolTrue := L.GetGlobal("bool_true")
+	assert.Equal(t, lua.LTBool, boolTrue.Type())
+	assert.True(t, bool(boolTrue.(lua.LBool)))
+
+	// Verify bool false
+	boolFalse := L.GetGlobal("bool_false")
+	assert.Equal(t, lua.LTBool, boolFalse.Type())
+	assert.False(t, bool(boolFalse.(lua.LBool)))
+
+	// Verify string
+	stringVal := L.GetGlobal("string_val")
+	assert.Equal(t, lua.LTString, stringVal.Type())
+	assert.Equal(t, "hello", string(stringVal.(lua.LString)))
+}
+
+// Test HTTP fetch with test server
+func TestFetchWithTestServer(t *testing.T) {
+	// Create test HTTP server
+	server := httptest.NewServer(http.HandlerFunc(func(w http.ResponseWriter, r *http.Request) {
+		// Verify request
+		assert.Equal(t, "GET", r.Method)
+		
+		// Send response
+		w.WriteHeader(http.StatusOK)
+		w.Write([]byte(`{"status": "success"}`))
+	}))
+	defer server.Close()
+
+	// Test fetch
+	L := lua.NewState()
+	defer L.Close()
+
+	L.SetGlobal("fetch", L.NewFunction(fetch))
+
+	script := `
+		response = fetch("` + server.URL + `")
+		assert(response ~= nil, "Expected response")
+		assert(response.ok == true, "Expected ok to be true")
+		assert(response.status == 200, "Expected status 200")
+		assert(response.body == '{"status": "success"}', "Expected correct body")
+	`
+
+	err := L.DoString(script)
+	assert.NoError(t, err)
+}
+
+func TestFetchWithTestServerPOST(t *testing.T) {
+	// Create test HTTP server
+	receivedBody := ""
+	server := httptest.NewServer(http.HandlerFunc(func(w http.ResponseWriter, r *http.Request) {
+		assert.Equal(t, "POST", r.Method)
+		assert.Equal(t, "application/json", r.Header.Get("Content-Type"))
+		
+		// Read body
+		buf := make([]byte, 1024)
+		n, _ := r.Body.Read(buf)
+		receivedBody = string(buf[:n])
+		
+		w.WriteHeader(http.StatusCreated)
+		w.Write([]byte(`{"created": true}`))
+	}))
+	defer server.Close()
+
+	L := lua.NewState()
+	defer L.Close()
+
+	L.SetGlobal("fetch", L.NewFunction(fetch))
+
+	script := `
+		local opts = {
+			method = "POST",
+			headers = {["Content-Type"] = "application/json"},
+			body = '{"test": "data"}'
+		}
+		response = fetch("` + server.URL + `", opts)
+		assert(response ~= nil, "Expected response")
+		assert(response.ok == true, "Expected ok to be true")
+		assert(response.status == 201, "Expected status 201")
+	`
+
+	err := L.DoString(script)
+	assert.NoError(t, err)
+	assert.Equal(t, `{"test": "data"}`, receivedBody)
+}
+
+func TestFetchWithTestServer404(t *testing.T) {
+	// Create test HTTP server that returns 404
+	server := httptest.NewServer(http.HandlerFunc(func(w http.ResponseWriter, r *http.Request) {
+		w.WriteHeader(http.StatusNotFound)
+		w.Write([]byte(`{"error": "not found"}`))
+	}))
+	defer server.Close()
+
+	L := lua.NewState()
+	defer L.Close()
+
+	L.SetGlobal("fetch", L.NewFunction(fetch))
+
+	script := `
+		response = fetch("` + server.URL + `")
+		assert(response ~= nil, "Expected response")
+		assert(response.ok == false, "Expected ok to be false for 404")
+		assert(response.status == 404, "Expected status 404")
+	`
+
+	err := L.DoString(script)
+	assert.NoError(t, err)
+}

processor/processor_helper_test.go

@@ -0,0 +1,366 @@
+package processor
+
+import (
+	"testing"
+
+	"github.com/stretchr/testify/assert"
+	lua "github.com/yuin/gopher-lua"
+)
+
+func TestSetVariables(t *testing.T) {
+	// Test with various variable types
+	vars := map[string]interface{}{
+		"multiplier": 2.5,
+		"prefix":     "TEST_",
+		"enabled":    true,
+		"count":      42,
+	}
+
+	SetVariables(vars)
+
+	// Create a new Lua state to verify variables are set
+	L, err := NewLuaState()
+	assert.NoError(t, err)
+	defer L.Close()
+
+	// Verify the variables are accessible
+	multiplier := L.GetGlobal("multiplier")
+	assert.Equal(t, lua.LTNumber, multiplier.Type())
+	assert.Equal(t, 2.5, float64(multiplier.(lua.LNumber)))
+
+	prefix := L.GetGlobal("prefix")
+	assert.Equal(t, lua.LTString, prefix.Type())
+	assert.Equal(t, "TEST_", string(prefix.(lua.LString)))
+
+	enabled := L.GetGlobal("enabled")
+	assert.Equal(t, lua.LTBool, enabled.Type())
+	assert.True(t, bool(enabled.(lua.LBool)))
+
+	count := L.GetGlobal("count")
+	assert.Equal(t, lua.LTNumber, count.Type())
+	assert.Equal(t, 42.0, float64(count.(lua.LNumber)))
+}
+
+func TestSetVariablesEmpty(t *testing.T) {
+	// Test with empty map
+	vars := map[string]interface{}{}
+	SetVariables(vars)
+
+	// Should not panic
+	L, err := NewLuaState()
+	assert.NoError(t, err)
+	defer L.Close()
+}
+
+func TestSetVariablesNil(t *testing.T) {
+	// Test with nil map
+	SetVariables(nil)
+
+	// Should not panic
+	L, err := NewLuaState()
+	assert.NoError(t, err)
+	defer L.Close()
+}
+
+func TestGetLuaFunctionsHelp(t *testing.T) {
+	help := GetLuaFunctionsHelp()
+
+	// Verify help is not empty
+	assert.NotEmpty(t, help)
+
+	// Verify it contains documentation for key functions
+	assert.Contains(t, help, "MATH FUNCTIONS")
+	assert.Contains(t, help, "STRING FUNCTIONS")
+	assert.Contains(t, help, "TABLE FUNCTIONS")
+	assert.Contains(t, help, "XML HELPER FUNCTIONS")
+	assert.Contains(t, help, "JSON HELPER FUNCTIONS")
+	assert.Contains(t, help, "HTTP FUNCTIONS")
+	assert.Contains(t, help, "REGEX FUNCTIONS")
+	assert.Contains(t, help, "UTILITY FUNCTIONS")
+	assert.Contains(t, help, "EXAMPLES")
+
+	// Verify specific functions are documented
+	assert.Contains(t, help, "min(a, b)")
+	assert.Contains(t, help, "max(a, b)")
+	assert.Contains(t, help, "round(x, n)")
+	assert.Contains(t, help, "fetch(url, options)")
+	assert.Contains(t, help, "findElements(root, tagName)")
+	assert.Contains(t, help, "visitJSON(data, callback)")
+	assert.Contains(t, help, "re(pattern, input)")
+	assert.Contains(t, help, "print(...)")
+}
+
+func TestFetchFunction(t *testing.T) {
+	L := lua.NewState()
+	defer L.Close()
+
+	// Register the fetch function
+	L.SetGlobal("fetch", L.NewFunction(fetch))
+
+	// Test 1: Missing URL should return nil and error
+	err := L.DoString(`
+		result, err = fetch("")
+		assert(result == nil, "Expected nil result for empty URL")
+		assert(err ~= nil, "Expected error for empty URL")
+	`)
+	assert.NoError(t, err)
+
+	// Test 2: Invalid URL should return error
+	err = L.DoString(`
+		result, err = fetch("not-a-valid-url")
+		assert(result == nil, "Expected nil result for invalid URL")
+		assert(err ~= nil, "Expected error for invalid URL")
+	`)
+	assert.NoError(t, err)
+}
+
+func TestFetchFunctionWithOptions(t *testing.T) {
+	L := lua.NewState()
+	defer L.Close()
+
+	// Register the fetch function
+	L.SetGlobal("fetch", L.NewFunction(fetch))
+
+	// Test with options (should fail gracefully with invalid URL)
+	err := L.DoString(`
+		local opts = {
+			method = "POST",
+			headers = {["Content-Type"] = "application/json"},
+			body = '{"test": "data"}'
+		}
+		result, err = fetch("http://invalid-domain-that-does-not-exist.local", opts)
+		-- Should get error due to invalid domain
+		assert(result == nil, "Expected nil result for invalid domain")
+		assert(err ~= nil, "Expected error for invalid domain")
+	`)
+	assert.NoError(t, err)
+}
+
+func TestPrependLuaAssignment(t *testing.T) {
+	tests := []struct {
+		name     string
+		input    string
+		expected string
+	}{
+		{
+			name:     "Simple assignment",
+			input:    "10",
+			expected: "v1 = 10",
+		},
+		{
+			name:     "Expression",
+			input:    "v1 * 2",
+			expected: "v1 = v1 * 2",
+		},
+		{
+			name:     "Assignment with equal sign",
+			input:    "= 5",
+			expected: "v1 = 5",
+		},
+		{
+			name:     "Complex expression",
+			input:    "math.floor(v1 / 2)",
+			expected: "v1 = math.floor(v1 / 2)",
+		},
+	}
+
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			result := PrependLuaAssignment(tt.input)
+			assert.Equal(t, tt.expected, result)
+		})
+	}
+}
+
+
+func TestBuildJSONLuaScript(t *testing.T) {
+	tests := []struct {
+		name     string
+		input    string
+		contains []string
+	}{
+		{
+			name:  "Simple JSON modification",
+			input: "data.value = data.value * 2; modified = true",
+			contains: []string{
+				"data.value = data.value * 2",
+				"modified = true",
+			},
+		},
+		{
+			name:  "Complex JSON script",
+			input: "for i, item in ipairs(data.items) do item.price = item.price * 1.5 end; modified = true",
+			contains: []string{
+				"for i, item in ipairs(data.items)",
+				"modified = true",
+			},
+		},
+	}
+
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			result := BuildJSONLuaScript(tt.input, "")
+			for _, substr := range tt.contains {
+				assert.Contains(t, result, substr)
+			}
+		})
+	}
+}
+
+func TestPrintToGo(t *testing.T) {
+	L := lua.NewState()
+	defer L.Close()
+
+	// Register the print function
+	L.SetGlobal("print", L.NewFunction(printToGo))
+
+	// Test printing various types
+	err := L.DoString(`
+		print("Hello, World!")
+		print(42)
+		print(true)
+		print(3.14)
+	`)
+	assert.NoError(t, err)
+}
+
+func TestEvalRegex(t *testing.T) {
+	L := lua.NewState()
+	defer L.Close()
+
+	// Register the regex function
+	L.SetGlobal("re", L.NewFunction(EvalRegex))
+
+	// Test 1: Simple match
+	err := L.DoString(`
+		matches = re("(\\d+)", "The answer is 42")
+		assert(matches ~= nil, "Expected matches")
+		assert(matches[1] == "42", "Expected full match to be 42")
+		assert(matches[2] == "42", "Expected capture group to be 42")
+	`)
+	assert.NoError(t, err)
+
+	// Test 2: No match
+	err = L.DoString(`
+		matches = re("(\\d+)", "No numbers here")
+		assert(matches == nil, "Expected nil for no match")
+	`)
+	assert.NoError(t, err)
+
+	// Test 3: Multiple capture groups
+	err = L.DoString(`
+		matches = re("(\\w+)\\s+(\\d+)", "item 123")
+		assert(matches ~= nil, "Expected matches")
+		assert(matches[1] == "item 123", "Expected full match")
+		assert(matches[2] == "item", "Expected first capture group")
+		assert(matches[3] == "123", "Expected second capture group")
+	`)
+	assert.NoError(t, err)
+}
+
+func TestEstimatePatternComplexity(t *testing.T) {
+	tests := []struct {
+		name        string
+		pattern     string
+		minExpected int
+	}{
+		{
+			name:        "Simple literal",
+			pattern:     "hello",
+			minExpected: 1,
+		},
+		{
+			name:        "With capture group",
+			pattern:     "(\\d+)",
+			minExpected: 2,
+		},
+		{
+			name:        "Complex pattern",
+			pattern:     "(?P<name>\\w+)\\s+(?P<value>\\d+\\.\\d+)",
+			minExpected: 3,
+		},
+	}
+
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			complexity := estimatePatternComplexity(tt.pattern)
+			assert.GreaterOrEqual(t, complexity, tt.minExpected)
+		})
+	}
+}
+
+
+func TestParseNumeric(t *testing.T) {
+	tests := []struct {
+		name      string
+		input     string
+		expected  float64
+		shouldOk  bool
+	}{
+		{"Integer", "42", 42.0, true},
+		{"Float", "3.14", 3.14, true},
+		{"Negative", "-10", -10.0, true},
+		{"Invalid", "not a number", 0, false},
+		{"Empty", "", 0, false},
+	}
+
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			result, ok := parseNumeric(tt.input)
+			assert.Equal(t, tt.shouldOk, ok)
+			if tt.shouldOk {
+				assert.Equal(t, tt.expected, result)
+			}
+		})
+	}
+}
+
+func TestFormatNumeric(t *testing.T) {
+	tests := []struct {
+		name     string
+		input    float64
+		expected string
+	}{
+		{"Integer value", 42.0, "42"},
+		{"Float value", 3.14, "3.14"},
+		{"Negative integer", -10.0, "-10"},
+		{"Negative float", -3.14, "-3.14"},
+		{"Zero", 0.0, "0"},
+	}
+
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			result := formatNumeric(tt.input)
+			assert.Equal(t, tt.expected, result)
+		})
+	}
+}
+
+func TestLuaHelperFunctionsDocumentation(t *testing.T) {
+	help := GetLuaFunctionsHelp()
+	
+	// All main function categories should be documented
+	expectedCategories := []string{
+		"MATH FUNCTIONS",
+		"STRING FUNCTIONS",
+		"XML HELPER FUNCTIONS",
+		"JSON HELPER FUNCTIONS",
+	}
+
+	for _, category := range expectedCategories {
+		assert.Contains(t, help, category, "Help should contain category: %s", category)
+	}
+
+	// Verify some key functions are mentioned
+	keyFunctions := []string{
+		"findElements",
+		"visitElements",
+		"visitJSON",
+		"round",
+		"fetch",
+	}
+
+	for _, fn := range keyFunctions {
+		assert.Contains(t, help, fn, "Help should mention function: %s", fn)
+	}
+}

processor/processor_test.go

@@ -0,0 +1,147 @@
+package processor_test
+
+import (
+	"testing"
+
+	"github.com/stretchr/testify/assert"
+	lua "github.com/yuin/gopher-lua"
+
+	"cook/processor"
+)
+
+// Happy Path: Function correctly returns all regex capture groups as Lua table when given valid pattern and input.
+func TestEvalRegex_CaptureGroupsReturned(t *testing.T) {
+	L := lua.NewState()
+	defer L.Close()
+	pattern := `(\w+)-(\d+)`
+	input := "test-42"
+	L.Push(lua.LString(pattern))
+	L.Push(lua.LString(input))
+
+	result := processor.EvalRegex(L)
+
+	assert.Equal(t, 1, result, "Expected return value to be 1 (one value pushed to Lua stack)")
+
+	out := L.Get(-1)
+	tbl, ok := out.(*lua.LTable)
+	if !ok {
+		t.Fatalf("Expected Lua table, got %T", out)
+	}
+	expected := []string{"test-42", "test", "42"}
+	for i, v := range expected {
+		val := tbl.RawGetInt(i + 1)
+		assert.Equal(t, lua.LString(v), val, "Expected index %d to be %q", i+1, v)
+	}
+}
+
+// Happy Path: Function returns nil when regex pattern does not match input string.
+func TestEvalRegex_NoMatchReturnsNil(t *testing.T) {
+	L := lua.NewState()
+	defer L.Close()
+	L.Push(lua.LString(`(foo)(bar)`))
+	L.Push(lua.LString("no-match-here"))
+
+	result := processor.EvalRegex(L)
+	assert.Equal(t, 1, result, "Expected return value to be 1 (one value pushed to Lua stack)")
+
+	out := L.Get(-1)
+	// Should be nil when no matches found
+	assert.Equal(t, lua.LNil, out, "Expected nil when no matches found")
+}
+
+// Happy Path: Function handles patterns with no capture groups by returning the full match in the Lua table.
+func TestEvalRegex_NoCaptureGroups(t *testing.T) {
+	L := lua.NewState()
+	defer L.Close()
+	pattern := `foo\d+`
+	input := "foo123"
+	L.Push(lua.LString(pattern))
+	L.Push(lua.LString(input))
+
+	result := processor.EvalRegex(L)
+	assert.Equal(t, 1, result, "Expected return value to be 1 (one value pushed to Lua stack)")
+
+	out := L.Get(-1)
+	tbl, ok := out.(*lua.LTable)
+	if !ok {
+		t.Fatalf("Expected Lua table, got %T", out)
+	}
+	fullMatch := tbl.RawGetInt(1)
+	assert.Equal(t, lua.LString("foo123"), fullMatch)
+	// There should be only the full match (index 1)
+	count := 0
+	tbl.ForEach(func(k, v lua.LValue) {
+		count++
+	})
+	assert.Equal(t, 1, count)
+}
+
+// Edge Case: Function handles invalid regex pattern by letting regexp.MustCompile panic (which is expected behavior)
+func TestEvalRegex_InvalidPattern(t *testing.T) {
+	L := lua.NewState()
+	defer L.Close()
+	pattern := `([a-z` // invalid regex
+	L.Push(lua.LString(pattern))
+	L.Push(lua.LString("someinput"))
+
+	// This should panic due to invalid regex pattern
+	assert.Panics(t, func() {
+		processor.EvalRegex(L)
+	}, "Expected panic for invalid regex pattern")
+}
+
+// Edge Case: Function returns nil when input string is empty and pattern doesn't match.
+func TestEvalRegex_EmptyInputString(t *testing.T) {
+	L := lua.NewState()
+	defer L.Close()
+	L.Push(lua.LString(`(foo)`))
+	L.Push(lua.LString(""))
+
+	result := processor.EvalRegex(L)
+	assert.Equal(t, 1, result, "Expected return value to be 1 (one value pushed to Lua stack)")
+
+	out := L.Get(-1)
+	// Should be nil when no matches found
+	assert.Equal(t, lua.LNil, out, "Expected nil when input is empty and pattern doesn't match")
+}
+
+// Edge Case: Function handles nil or missing arguments gracefully without causing a runtime panic.
+func TestEvalRegex_MissingArguments(t *testing.T) {
+	L := lua.NewState()
+	defer L.Close()
+	defer func() {
+		if r := recover(); r != nil {
+			t.Errorf("Did not expect panic when arguments are missing, got: %v", r)
+		}
+	}()
+	// No arguments pushed at all
+	processor.EvalRegex(L)
+	// Should just not match anything or produce empty table, but must not panic
+}
+
+func TestEvalComplexRegex(t *testing.T) {
+	// Test complex regex pattern with multiple capture groups
+	L := lua.NewState()
+	defer L.Close()
+	pattern := `^((Bulk_)?(Pistol|Rifle).*?Round.*?)$`
+	input := "Pistol_Round"
+	L.Push(lua.LString(pattern))
+	L.Push(lua.LString(input))
+
+	processor.EvalRegex(L)
+
+	out := L.Get(-1)
+	tbl, ok := out.(*lua.LTable)
+	if !ok {
+		t.Fatalf("Expected Lua table, got %T", out)
+	}
+
+	// Pattern should match: ["Pistol_Round", "Pistol_Round", "", "Pistol"]
+	// This creates 4 elements in the matches array, not 1
+	expectedCount := 4
+	actualCount := 0
+	tbl.ForEach(func(k, v lua.LValue) {
+		actualCount++
+	})
+	assert.Equal(t, expectedCount, actualCount, "Expected %d matches for pattern %q with input %q", expectedCount, pattern, input)
+}

processor/regex.go

@@ -1,18 +1,20 @@
 package processor
 
 import (
+	"cook/utils"
 	"fmt"
 	"regexp"
 	"strconv"
 	"strings"
 	"time"
 
+	logger "git.site.quack-lab.dev/dave/cylogger"
 	lua "github.com/yuin/gopher-lua"
-
-	"modify/logger"
-	"modify/utils"
 )
 
+// regexLogger is a scoped logger for the processor/regex package.
+var regexLogger = logger.Default.WithPrefix("processor/regex")
+
 type CaptureGroup struct {
 	Name    string
 	Value   string
@@ -20,49 +22,63 @@ type CaptureGroup struct {
 	Range   [2]int
 }
 
-// ProcessContent applies regex replacement with Lua processing
-func ProcessRegex(content string, command utils.ModifyCommand) ([]utils.ReplaceCommand, error) {
-	var commands []utils.ReplaceCommand
-	logger.Trace("Processing regex: %q", command.Regex)
+// ProcessRegex applies regex replacement with Lua processing.
+// The filename here exists ONLY so we can pass it to the lua environment.
+// It's not used for anything else.
+func ProcessRegex(content string, command utils.ModifyCommand, filename string) ([]utils.ReplaceCommand, error) {
+	processRegexLogger := regexLogger.WithPrefix("ProcessRegex").WithField("commandName", command.Name).WithField("file", filename)
+	processRegexLogger.Debug("Starting regex processing for file")
+	processRegexLogger.Trace("Initial file content length: %d", len(content))
+	processRegexLogger.Trace("Command details: %+v", command)
 
+	var commands []utils.ReplaceCommand
 	// Start timing the regex processing
 	startTime := time.Now()
 
 	// We don't HAVE to do this multiple times for a pattern
 	// But it's quick enough for us to not care
 	pattern := resolveRegexPlaceholders(command.Regex)
-	logger.Debug("Compiling regex pattern: %s", pattern)
+	processRegexLogger.Debug("Resolved regex placeholders. Pattern: %s", pattern)
+
+	// I'm not too happy about having to trim regex, we could have meaningful whitespace or newlines
+	// But it's a compromise that allows us to use | in yaml
+	// Otherwise we would have to escape every god damn pair of quotation marks
+	// And a bunch of other shit
+	pattern = strings.TrimSpace(pattern)
+	processRegexLogger.Debug("Trimmed regex pattern: %s", pattern)
 
 	patternCompileStart := time.Now()
 	compiledPattern, err := regexp.Compile(pattern)
 	if err != nil {
-		logger.Error("Error compiling pattern: %v", err)
+		processRegexLogger.Error("Error compiling pattern %q: %v", pattern, err)
 		return commands, fmt.Errorf("error compiling pattern: %v", err)
 	}
-	logger.Debug("Compiled pattern successfully in %v: %s", time.Since(patternCompileStart), pattern)
+	processRegexLogger.Debug("Compiled pattern successfully in %v. Pattern: %s", time.Since(patternCompileStart), pattern)
 
 	// Same here, it's just string concatenation, it won't kill us
 	// More important is that we don't fuck up the command
 	// But we shouldn't be able to since it's passed by value
-	previous := command.Lua
-	luaExpr := BuildLuaScript(command.Lua)
-	logger.Debug("Transformed Lua expression: %q → %q", previous, luaExpr)
+	previousLuaExpr := command.Lua
+	luaExpr := BuildLuaScript(command.Lua, command.SourceDir)
+	processRegexLogger.Debug("Transformed Lua expression: %q → %q", previousLuaExpr, luaExpr)
+	processRegexLogger.Trace("Full Lua script: %q", utils.LimitString(luaExpr, 200))
 
 	// Process all regex matches
 	matchFindStart := time.Now()
 	indices := compiledPattern.FindAllStringSubmatchIndex(content, -1)
 	matchFindDuration := time.Since(matchFindStart)
 
-	logger.Debug("Found %d matches in content of length %d (search took %v)",
+	processRegexLogger.Debug("Found %d matches in content of length %d (search took %v)",
 		len(indices), len(content), matchFindDuration)
+	processRegexLogger.Trace("Match indices: %v", indices)
 
 	// Log pattern complexity metrics
 	patternComplexity := estimatePatternComplexity(pattern)
-	logger.Debug("Pattern complexity estimate: %d", patternComplexity)
+	processRegexLogger.Debug("Pattern complexity estimate: %d", patternComplexity)
 
 	if len(indices) == 0 {
-		logger.Warning("No matches found for regex: %q", pattern)
-		logger.Debug("Total regex processing time: %v", time.Since(startTime))
+		processRegexLogger.Warning("No matches found for regex: %s", pattern)
+		processRegexLogger.Debug("Total regex processing time: %v", time.Since(startTime))
 		return commands, nil
 	}
 
@@ -71,19 +87,21 @@ func ProcessRegex(content string, command utils.ModifyCommand) ([]utils.ReplaceC
 	// By going backwards we fuck up all the indices to the end of the file that we don't care about
 	// Because there either aren't any (last match) or they're already modified (subsequent matches)
 	for i, matchIndices := range indices {
-		logger.Debug("Processing match %d of %d", i+1, len(indices))
-		logger.Trace("Match indices: %v (match position %d-%d)", matchIndices, matchIndices[0], matchIndices[1])
+		matchLogger := processRegexLogger.WithField("matchNum", i+1)
+		matchLogger.Debug("Processing match %d of %d", i+1, len(indices))
+		matchLogger.Trace("Match indices: %v (match position %d-%d)", matchIndices, matchIndices[0], matchIndices[1])
 
 		L, err := NewLuaState()
 		if err != nil {
-			logger.Error("Error creating Lua state: %v", err)
+			matchLogger.Error("Error creating Lua state: %v", err)
 			return commands, fmt.Errorf("error creating Lua state: %v", err)
 		}
+		L.SetGlobal("file", lua.LString(filename))
 		// Hmm... Maybe we don't want to defer this..
 		// Maybe we want to close them every iteration
 		// We'll leave it as is for now
 		defer L.Close()
-		logger.Trace("Lua state created successfully for match %d", i+1)
+		matchLogger.Trace("Lua state created successfully for match %d", i+1)
 
 		// Why we're doing this whole song and dance of indices is to properly handle empty matches
 		// Plus it's a little cleaner to surgically replace our matches
@@ -92,20 +110,17 @@ func ProcessRegex(content string, command utils.ModifyCommand) ([]utils.ReplaceC
 		// So when we're cutting open the array we say 0:7 + modified + 7:end
 		// As if concatenating in the middle of the array
 		// Plus it supports lookarounds
-		match := content[matchIndices[0]:matchIndices[1]]
-		matchPreview := match
-		if len(match) > 50 {
-			matchPreview = match[:47] + "..."
-		}
-		logger.Trace("Matched content: %q (length: %d)", matchPreview, len(match))
+		matchContent := content[matchIndices[0]:matchIndices[1]]
+		matchPreview := utils.LimitString(matchContent, 50)
+		matchLogger.Trace("Matched content: %q (length: %d)", matchPreview, len(matchContent))
 
 		groups := matchIndices[2:]
 		if len(groups) <= 0 {
-			logger.Warning("No capture groups found for match %q and regex %q", matchPreview, pattern)
+			matchLogger.Warning("No capture groups found for match %q and regex %q", matchPreview, pattern)
 			continue
 		}
 		if len(groups)%2 == 1 {
-			logger.Warning("Invalid number of group indices (%d), should be even: %v", len(groups), groups)
+			matchLogger.Warning("Invalid number of group indices (%d), should be even: %v", len(groups), groups)
 			continue
 		}
 
@@ -116,11 +131,11 @@ func ProcessRegex(content string, command utils.ModifyCommand) ([]utils.ReplaceC
 				validGroups++
 			}
 		}
-		logger.Debug("Found %d valid capture groups in match", validGroups)
+		matchLogger.Debug("Found %d valid capture groups in match", validGroups)
 
 		for _, index := range groups {
 			if index == -1 {
-				logger.Warning("Negative index encountered in match indices %v. This may indicate an issue with the regex pattern or an empty/optional capture group.", matchIndices)
+				matchLogger.Warning("Negative index encountered in match indices %v. This may indicate an issue with the regex pattern or an empty/optional capture group.", matchIndices)
 				continue
 			}
 		}
@@ -135,6 +150,7 @@ func ProcessRegex(content string, command utils.ModifyCommand) ([]utils.ReplaceC
 			start := groups[i*2]
 			end := groups[i*2+1]
 			if start == -1 || end == -1 {
+				matchLogger.Debug("Skipping empty or unmatched capture group #%d (name: %q)", i+1, name)
 				continue
 			}
 
@@ -147,71 +163,77 @@ func ProcessRegex(content string, command utils.ModifyCommand) ([]utils.ReplaceC
 
 			// Include name info in log if available
 			if name != "" {
-				logger.Trace("Capture group '%s': %q (pos %d-%d)", name, value, start, end)
+				matchLogger.Trace("Capture group '%s': %q (pos %d-%d)", name, value, start, end)
 			} else {
-				logger.Trace("Capture group #%d: %q (pos %d-%d)", i+1, value, start, end)
+				matchLogger.Trace("Capture group #%d: %q (pos %d-%d)", i+1, value, start, end)
 			}
 		}
 
-		captureGroups = deduplicateGroups(captureGroups)
+		// Use the DeduplicateGroups flag to control whether to deduplicate capture groups
+		if !command.NoDedup {
+			matchLogger.Debug("Deduplicating capture groups as specified in command settings")
+			captureGroups = deduplicateGroups(captureGroups)
+			matchLogger.Trace("Capture groups after deduplication: %v", captureGroups)
+		} else {
+			matchLogger.Debug("Skipping deduplication of capture groups (NoDedup is true)")
+		}
 
 		if err := toLua(L, captureGroups); err != nil {
-			logger.Error("Failed to set Lua variables: %v", err)
+			matchLogger.Error("Failed to set Lua variables for capture groups: %v", err)
 			continue
 		}
-		logger.Trace("Set %d capture groups as Lua variables", len(captureGroups))
+		matchLogger.Debug("Set %d capture groups as Lua variables", len(captureGroups))
+		matchLogger.Trace("Lua globals set for capture groups")
 
 		if err := L.DoString(luaExpr); err != nil {
-			logger.Error("Lua script execution failed: %v\nScript: %s\nCapture Groups: %+v",
-				err, luaExpr, captureGroups)
+			matchLogger.Error("Lua script execution failed: %v\nScript: %s\nCapture Groups: %+v",
+				err, utils.LimitString(luaExpr, 200), captureGroups)
 			continue
 		}
-		logger.Trace("Lua script executed successfully")
+		matchLogger.Debug("Lua script executed successfully")
 
 		// Get modifications from Lua
-		captureGroups, err = fromLua(L, captureGroups)
+		updatedCaptureGroups, err := fromLua(L, captureGroups)
 		if err != nil {
-			logger.Error("Failed to retrieve modifications from Lua: %v", err)
+			matchLogger.Error("Failed to retrieve modifications from Lua: %v", err)
 			continue
 		}
-		logger.Trace("Retrieved updated values from Lua")
+		matchLogger.Debug("Retrieved updated values from Lua")
+		matchLogger.Trace("Updated capture groups from Lua: %v", updatedCaptureGroups)
 
 		replacement := ""
 		replacementVar := L.GetGlobal("replacement")
 		if replacementVar.Type() != lua.LTNil {
 			replacement = replacementVar.String()
-			logger.Debug("Using global replacement: %q", replacement)
+			matchLogger.Debug("Using global replacement variable from Lua: %q", replacement)
 		}
 
 		// Check if modification flag is set
 		modifiedVal := L.GetGlobal("modified")
 		if modifiedVal.Type() != lua.LTBool || !lua.LVAsBool(modifiedVal) {
-			logger.Debug("Skipping match - no modifications made by Lua script")
+			matchLogger.Debug("Skipping match - no modifications indicated by Lua script")
 			continue
 		}
 
 		if replacement == "" {
-			// Apply the modifications to the original match
-			replacement = match
-
 			// Count groups that were actually modified
-			modifiedGroups := 0
-			for _, capture := range captureGroups {
+			modifiedGroupsCount := 0
+			for _, capture := range updatedCaptureGroups {
 				if capture.Value != capture.Updated {
-					modifiedGroups++
+					modifiedGroupsCount++
 				}
 			}
-			logger.Info("%d of %d capture groups identified for modification", modifiedGroups, len(captureGroups))
+			matchLogger.Info("%d of %d capture groups identified for modification", modifiedGroupsCount, len(updatedCaptureGroups))
 
-			for _, capture := range captureGroups {
+			for _, capture := range updatedCaptureGroups {
 				if capture.Value == capture.Updated {
-					logger.Info("Capture group unchanged: %s", capture.Value)
+					matchLogger.Debug("Capture group unchanged: %s", utils.LimitString(capture.Value, 50))
 					continue
 				}
 
 				// Log what changed with context
-				logger.Debug("Capture group %s scheduled for modification: %q → %q",
-					capture.Name, capture.Value, capture.Updated)
+				matchLogger.Debug("Capture group %q scheduled for modification: %q → %q",
+					capture.Name, utils.LimitString(capture.Value, 50), utils.LimitString(capture.Updated, 50))
 
 				// Indices of the group are relative to content
 				// To relate them to match we have to subtract the match start index
@@ -221,42 +243,57 @@ func ProcessRegex(content string, command utils.ModifyCommand) ([]utils.ReplaceC
 					To:   capture.Range[1],
 					With: capture.Updated,
 				})
+				matchLogger.Trace("Added replacement command: %+v", commands[len(commands)-1])
 			}
 		} else {
+			matchLogger.Debug("Using full replacement string from Lua: %q", utils.LimitString(replacement, 50))
 			commands = append(commands, utils.ReplaceCommand{
 				From: matchIndices[0],
 				To:   matchIndices[1],
 				With: replacement,
 			})
+			matchLogger.Trace("Added full replacement command: %+v", commands[len(commands)-1])
 		}
 	}
 
-	logger.Debug("Total regex processing time: %v", time.Since(startTime))
+	processRegexLogger.Debug("Total regex processing time: %v", time.Since(startTime))
+	processRegexLogger.Debug("Generated %d total modifications", len(commands))
 	return commands, nil
 }
 
 func deduplicateGroups(captureGroups []*CaptureGroup) []*CaptureGroup {
-	deduplicatedGroups := make([]*CaptureGroup, 0)
+	deduplicateGroupsLogger := regexLogger.WithPrefix("deduplicateGroups")
+	deduplicateGroupsLogger.Debug("Starting deduplication of capture groups")
+	deduplicateGroupsLogger.Trace("Input capture groups: %v", captureGroups)
+
+	// Preserve input order and drop any group that overlaps with an already accepted group
+	accepted := make([]*CaptureGroup, 0, len(captureGroups))
 	for _, group := range captureGroups {
+		groupLogger := deduplicateGroupsLogger.WithField("groupName", group.Name).WithField("groupRange", group.Range)
+		groupLogger.Debug("Processing capture group")
+
 		overlaps := false
-		logger.Debug("Checking capture group: %s with range %v", group.Name, group.Range)
-		for _, existingGroup := range deduplicatedGroups {
-			logger.Debug("Comparing with existing group: %s with range %v", existingGroup.Name, existingGroup.Range)
-			if group.Range[0] < existingGroup.Range[1] && group.Range[1] > existingGroup.Range[0] {
+		for _, kept := range accepted {
+			// Overlap if start < keptEnd and end > keptStart (adjacent is allowed)
+			if group.Range[0] < kept.Range[1] && group.Range[1] > kept.Range[0] {
 				overlaps = true
-				logger.Warning("Detected overlap between capture group '%s' and existing group '%s' in range %v-%v and %v-%v", group.Name, existingGroup.Name, group.Range[0], group.Range[1], existingGroup.Range[0], existingGroup.Range[1])
 				break
 			}
 		}
+
 		if overlaps {
-			// We CAN just continue despite this fuckup
-			logger.Error("Overlapping capture group: %s", group.Name)
+			groupLogger.Warning("Overlapping capture group detected and skipped.")
 			continue
 		}
-		logger.Debug("No overlap detected for capture group: %s. Adding to deduplicated groups.", group.Name)
-		deduplicatedGroups = append(deduplicatedGroups, group)
+
+		groupLogger.Debug("Capture group does not overlap with previously accepted groups. Adding.")
+		accepted = append(accepted, group)
 	}
-	return deduplicatedGroups
+
+	deduplicateGroupsLogger.Debug("Finished deduplication. Original %d groups, %d deduplicated.", len(captureGroups), len(accepted))
+	deduplicateGroupsLogger.Trace("Deduplicated groups: %v", accepted)
+
+	return accepted
 }
 
 // The order of these replaces is important
@@ -265,107 +302,186 @@ func deduplicateGroups(captureGroups []*CaptureGroup) []*CaptureGroup {
 // Expand to another capture group in the capture group
 // We really only want one (our named) capture group
 func resolveRegexPlaceholders(pattern string) string {
+	resolveLogger := regexLogger.WithPrefix("resolveRegexPlaceholders").WithField("originalPattern", utils.LimitString(pattern, 100))
+	resolveLogger.Debug("Resolving regex placeholders in pattern")
+
 	// Handle special pattern modifications
 	if !strings.HasPrefix(pattern, "(?s)") {
 		pattern = "(?s)" + pattern
-		// Use fmt.Printf for test compatibility
-		fmt.Printf("Pattern modified to include (?s): %s\n", pattern)
+		resolveLogger.Debug("Prepended '(?s)' to pattern for single-line mode")
 	}
 
 	namedGroupNum := regexp.MustCompile(`(?:(\?<[^>]+>)(!num))`)
 	pattern = namedGroupNum.ReplaceAllStringFunc(pattern, func(match string) string {
+		funcLogger := resolveLogger.WithPrefix("namedGroupNumReplace").WithField("match", utils.LimitString(match, 50))
+		funcLogger.Debug("Processing named group !num placeholder")
 		parts := namedGroupNum.FindStringSubmatch(match)
 		if len(parts) != 3 {
+			funcLogger.Warning("Unexpected number of submatches for namedGroupNum: %d. Returning original match.", len(parts))
 			return match
 		}
 		replacement := `-?\d*\.?\d+`
+		funcLogger.Trace("Replacing !num in named group with: %q", replacement)
 		return parts[1] + replacement
 	})
+	resolveLogger.Debug("Handled named group !num placeholders")
+
 	pattern = strings.ReplaceAll(pattern, "!num", `(-?\d*\.?\d+)`)
+	resolveLogger.Debug("Replaced !num with numeric capture group")
+
 	pattern = strings.ReplaceAll(pattern, "!any", `.*?`)
+	resolveLogger.Debug("Replaced !any with non-greedy wildcard")
+
+	pattern = strings.ReplaceAll(pattern, "\n", "\r?\n")
+	resolveLogger.Debug("Added optional carriage return support for Windows line endings")
+
 	repPattern := regexp.MustCompile(`!rep\(([^,]+),\s*(\d+)\)`)
 	// !rep(pattern, count) repeats the pattern n times
 	// Inserting !any between each repetition
 	pattern = repPattern.ReplaceAllStringFunc(pattern, func(match string) string {
+		funcLogger := resolveLogger.WithPrefix("repPatternReplace").WithField("match", utils.LimitString(match, 50))
+		funcLogger.Debug("Processing !rep placeholder")
 		parts := repPattern.FindStringSubmatch(match)
 		if len(parts) != 3 {
+			funcLogger.Warning("Unexpected number of submatches for repPattern: %d. Returning original match.", len(parts))
 			return match
 		}
 		repeatedPattern := parts[1]
-		count := parts[2]
-		repetitions, _ := strconv.Atoi(count)
-		return strings.Repeat(repeatedPattern+".*?", repetitions-1) + repeatedPattern
+		countStr := parts[2]
+		repetitions, err := strconv.Atoi(countStr)
+		if err != nil {
+			funcLogger.Error("Failed to parse repetition count %q: %v. Returning original match.", countStr, err)
+			return match
+		}
+
+		var finalReplacement string
+		if repetitions > 0 {
+			finalReplacement = strings.Repeat(repeatedPattern+".*?", repetitions-1) + repeatedPattern
+		} else {
+			finalReplacement = ""
+		}
+
+		funcLogger.Trace("Replaced !rep with %d repetitions of %q: %q", repetitions, utils.LimitString(repeatedPattern, 30), utils.LimitString(finalReplacement, 100))
+		return finalReplacement
 	})
+	resolveLogger.Debug("Handled !rep placeholders")
+
+	resolveLogger.Debug("Finished resolving regex placeholders")
+	resolveLogger.Trace("Final resolved pattern: %q", utils.LimitString(pattern, 100))
 	return pattern
 }
 
 // ToLua sets capture groups as Lua variables (v1, v2, etc. for numeric values and s1, s2, etc. for strings)
 func toLua(L *lua.LState, data interface{}) error {
+	toLuaLogger := regexLogger.WithPrefix("toLua")
+	toLuaLogger.Debug("Setting capture groups as Lua variables")
+
 	captureGroups, ok := data.([]*CaptureGroup)
 	if !ok {
+		toLuaLogger.Error("Invalid data type for toLua. Expected []*CaptureGroup, got %T", data)
 		return fmt.Errorf("expected []*CaptureGroup for captures, got %T", data)
 	}
+	toLuaLogger.Trace("Input capture groups: %v", captureGroups)
 
 	groupindex := 0
 	for _, capture := range captureGroups {
+		groupLogger := toLuaLogger.WithField("captureGroup", capture.Name).WithField("value", utils.LimitString(capture.Value, 50))
+		groupLogger.Debug("Processing capture group for Lua")
+
 		if capture.Name == "" {
 			// We don't want to change the name of the capture group
 			// Even if it's empty
 			tempName := fmt.Sprintf("%d", groupindex+1)
 			groupindex++
+			groupLogger.Debug("Unnamed capture group, assigning temporary name: %q", tempName)
 
 			L.SetGlobal("s"+tempName, lua.LString(capture.Value))
+			groupLogger.Trace("Set Lua global s%s = %q", tempName, capture.Value)
 
 			val, err := strconv.ParseFloat(capture.Value, 64)
 			if err == nil {
 				L.SetGlobal("v"+tempName, lua.LNumber(val))
+				groupLogger.Trace("Set Lua global v%s = %f", tempName, val)
+			} else {
+				groupLogger.Trace("Value %q is not numeric, skipping v%s assignment", capture.Value, tempName)
 			}
 		} else {
 			val, err := strconv.ParseFloat(capture.Value, 64)
 			if err == nil {
 				L.SetGlobal(capture.Name, lua.LNumber(val))
+				groupLogger.Trace("Set Lua global %s = %f (numeric)", capture.Name, val)
 			} else {
 				L.SetGlobal(capture.Name, lua.LString(capture.Value))
+				groupLogger.Trace("Set Lua global %s = %q (string)", capture.Name, capture.Value)
 			}
 		}
 	}
 
+	toLuaLogger.Debug("Finished setting capture groups as Lua variables")
 	return nil
 }
 
 // FromLua implements the Processor interface for RegexProcessor
 func fromLua(L *lua.LState, captureGroups []*CaptureGroup) ([]*CaptureGroup, error) {
+	fromLuaLogger := regexLogger.WithPrefix("fromLua")
+	fromLuaLogger.Debug("Retrieving modifications from Lua for capture groups")
+	fromLuaLogger.Trace("Initial capture groups: %v", captureGroups)
+
 	captureIndex := 0
 	for _, capture := range captureGroups {
-		if capture.Name == "" {
-			capture.Name = fmt.Sprintf("%d", captureIndex+1)
+		groupLogger := fromLuaLogger.WithField("originalCaptureName", capture.Name).WithField("originalValue", utils.LimitString(capture.Value, 50))
+		groupLogger.Debug("Processing capture group to retrieve updated value")
 
-			vVarName := fmt.Sprintf("v%s", capture.Name)
-			sVarName := fmt.Sprintf("s%s", capture.Name)
+		if capture.Name == "" {
+			// This case means it was an unnamed capture group originally.
+			// We need to reconstruct the original temporary name to fetch its updated value.
+			// The name will be set to an integer if it was empty, then incremented.
+			// So, we use the captureIndex to get the correct 'vX' and 'sX' variables.
+			tempName := fmt.Sprintf("%d", captureIndex+1)
+			groupLogger.Debug("Retrieving updated value for unnamed group (temp name: %q)", tempName)
+
+			vVarName := fmt.Sprintf("v%s", tempName)
+			sVarName := fmt.Sprintf("s%s", tempName)
 			captureIndex++
 
 			vLuaVal := L.GetGlobal(vVarName)
 			sLuaVal := L.GetGlobal(sVarName)
 
+			groupLogger.Trace("Lua values for unnamed group: v=%v, s=%v", vLuaVal, sLuaVal)
+
 			if sLuaVal.Type() == lua.LTString {
 				capture.Updated = sLuaVal.String()
+				groupLogger.Trace("Updated value from s%s (string): %q", tempName, capture.Updated)
 			}
 			// Numbers have priority
 			if vLuaVal.Type() == lua.LTNumber {
 				capture.Updated = vLuaVal.String()
+				groupLogger.Trace("Updated value from v%s (numeric): %q", tempName, capture.Updated)
 			}
 		} else {
-			// Easy shit
-			capture.Updated = L.GetGlobal(capture.Name).String()
+			// Easy shit, directly use the named capture group
+			updatedValue := L.GetGlobal(capture.Name)
+			if updatedValue.Type() != lua.LTNil {
+				capture.Updated = updatedValue.String()
+				groupLogger.Trace("Updated value for named group %q: %q", capture.Name, capture.Updated)
+			} else {
+				groupLogger.Debug("Named capture group %q not found in Lua globals or is nil. Keeping original value.", capture.Name)
+				capture.Updated = capture.Value // Keep original if not found or nil
+			}
 		}
+		groupLogger.Debug("Finished processing capture group. Original: %q, Updated: %q", utils.LimitString(capture.Value, 50), utils.LimitString(capture.Updated, 50))
 	}
 
+	fromLuaLogger.Debug("Finished retrieving modifications from Lua")
+	fromLuaLogger.Trace("Final updated capture groups: %v", captureGroups)
 	return captureGroups, nil
 }
 
 // estimatePatternComplexity gives a rough estimate of regex pattern complexity
 // This can help identify potentially problematic patterns
 func estimatePatternComplexity(pattern string) int {
+	estimateComplexityLogger := regexLogger.WithPrefix("estimatePatternComplexity").WithField("pattern", utils.LimitString(pattern, 100))
+	estimateComplexityLogger.Debug("Estimating regex pattern complexity")
 	complexity := len(pattern)
 
 	// Add complexity for potentially expensive operations
@@ -378,5 +494,6 @@ func estimatePatternComplexity(pattern string) int {
 	complexity += strings.Count(pattern, "\\1") * 3 // Backreferences
 	complexity += strings.Count(pattern, "{") * 2   // Counted repetition
 
+	estimateComplexityLogger.Debug("Estimated pattern complexity: %d", complexity)
 	return complexity
 }

processor/regex_coverage_test.go

@@ -0,0 +1,87 @@
+package processor
+
+import (
+	"cook/utils"
+	"regexp"
+	"testing"
+
+	"github.com/stretchr/testify/assert"
+)
+
+// Test named capture group fallback when value is not in Lua
+func TestNamedCaptureGroupFallback(t *testing.T) {
+	pattern := `value = (?P<myvalue>\d+)`
+	input := `value = 42`
+	// Don't set myvalue in Lua, but do something else so we get a match
+	lua := `v1 = v1 * 2 -- Set v1 but not myvalue, test fallback`
+
+	cmd := utils.ModifyCommand{
+		Name:  "test_fallback",
+		Regex: pattern,
+		Lua:   lua,
+	}
+
+	re := regexp.MustCompile(pattern)
+	matches := re.FindStringSubmatchIndex(input)
+	assert.NotNil(t, matches)
+
+	replacements, err := ProcessRegex(input, cmd, "test.txt")
+	
+	// Should not error
+	assert.NoError(t, err)
+	
+	// Since only v1 is set, myvalue should keep original
+	// Should have 1 replacement for v1
+	if replacements != nil {
+		assert.GreaterOrEqual(t, len(replacements), 0)
+	}
+}
+
+// Test named capture groups with nil value in Lua
+func TestNamedCaptureGroupNilInLua(t *testing.T) {
+	pattern := `value = (?P<num>\d+)`
+	input := `value = 123`
+	// Set num to nil explicitly, and also set v1 to get a modification
+	lua := `v1 = v1 .. "_test"; num = nil -- v1 modified, num set to nil`
+
+	cmd := utils.ModifyCommand{
+		Name:  "test_nil",
+		Regex: pattern,
+		Lua:   lua,
+	}
+
+	replacements, err := ProcessRegex(input, cmd, "test.txt")
+	
+	// Should not error
+	assert.NoError(t, err)
+	
+	// Should have replacements for v1, num should fallback to original
+	if replacements != nil {
+		assert.GreaterOrEqual(t, len(replacements), 0)
+	}
+}
+
+// Test multiple named capture groups with some undefined
+func TestMixedNamedCaptureGroups(t *testing.T) {
+	pattern := `(?P<key>\w+) = (?P<value>\d+)`
+	input := `count = 100`
+	lua := `key = key .. "_modified" -- Only modify key, leave value undefined`
+
+	cmd := utils.ModifyCommand{
+		Name:  "test_mixed",
+		Regex: pattern,
+		Lua:   lua,
+	}
+
+	replacements, err := ProcessRegex(input, cmd, "test.txt")
+	
+	assert.NoError(t, err)
+	assert.NotNil(t, replacements)
+	
+	// Apply replacements
+	result, _ := utils.ExecuteModifications(replacements, input)
+	
+	// key should be modified, value should remain unchanged
+	assert.Contains(t, result, "count_modified")
+	assert.Contains(t, result, "100")
+}

processor/regex_test.go

@@ -2,9 +2,8 @@ package processor
 
 import (
 	"bytes"
-	"fmt"
+	"cook/utils"
 	"io"
-	"modify/utils"
 	"os"
 	"regexp"
 	"strings"
@@ -31,14 +30,14 @@ func normalizeWhitespace(s string) string {
 	return re.ReplaceAllString(strings.TrimSpace(s), " ")
 }
 
-func ApiAdaptor(content string, regex string, lua string) (string, int, int, error) {
+func APIAdaptor(content string, regex string, lua string) (string, int, int, error) {
 	command := utils.ModifyCommand{
 		Regex:    regex,
 		Lua:      lua,
 		LogLevel: "TRACE",
 	}
 
-	commands, err := ProcessRegex(content, command)
+	commands, err := ProcessRegex(content, command, "test")
 	if err != nil {
 		return "", 0, 0, err
 	}
@@ -80,7 +79,7 @@ func TestSimpleValueMultiplication(t *testing.T) {
     </item>
 </config>`
 
-	result, mods, matches, err := ApiAdaptor(content, `(?s)<value>(\d+)</value>`, "v1 = v1*1.5")
+	result, mods, matches, err := APIAdaptor(content, `(?s)<value>(\d+)</value>`, "v1 = v1*1.5")
 
 	assert.NoError(t, err, "Error processing content: %v", err)
 	assert.Equal(t, 1, matches, "Expected 1 match, got %d", matches)
@@ -101,7 +100,7 @@ func TestShorthandNotation(t *testing.T) {
     </item>
 </config>`
 
-	result, mods, matches, err := ApiAdaptor(content, `(?s)<value>(\d+)</value>`, "v1*1.5")
+	result, mods, matches, err := APIAdaptor(content, `(?s)<value>(\d+)</value>`, "v1*1.5")
 
 	assert.NoError(t, err, "Error processing content: %v", err)
 	assert.Equal(t, 1, matches, "Expected 1 match, got %d", matches)
@@ -122,7 +121,7 @@ func TestShorthandNotationFloats(t *testing.T) {
     </item>
 </config>`
 
-	result, mods, matches, err := ApiAdaptor(content, `(?s)<value>(\d+\.\d+)</value>`, "v1*1.5")
+	result, mods, matches, err := APIAdaptor(content, `(?s)<value>(\d+\.\d+)</value>`, "v1*1.5")
 
 	assert.NoError(t, err, "Error processing content: %v", err)
 	assert.Equal(t, 1, matches, "Expected 1 match, got %d", matches)
@@ -147,7 +146,7 @@ func TestArrayNotation(t *testing.T) {
     </prices>
 </config>`
 
-	result, mods, matches, err := ApiAdaptor(content, `(?s)<price>(\d+)</price>`, "v1*2")
+	result, mods, matches, err := APIAdaptor(content, `(?s)<price>(\d+)</price>`, "v1*2")
 
 	assert.NoError(t, err, "Error processing content: %v", err)
 	assert.Equal(t, 3, matches, "Expected 3 matches, got %d", matches)
@@ -168,7 +167,7 @@ func TestMultipleNumericMatches(t *testing.T) {
     <entry>400</entry>
 </data>`
 
-	result, mods, matches, err := ApiAdaptor(content, `<entry>(\d+)</entry>`, "v1*2")
+	result, mods, matches, err := APIAdaptor(content, `<entry>(\d+)</entry>`, "v1*2")
 
 	assert.NoError(t, err, "Error processing content: %v", err)
 	assert.Equal(t, 3, matches, "Expected 3 matches, got %d", matches)
@@ -187,7 +186,7 @@ func TestMultipleStringMatches(t *testing.T) {
     <name>Mary_modified</name>
 </data>`
 
-	result, mods, matches, err := ApiAdaptor(content, `<name>([A-Za-z]+)</name>`, `s1 = s1 .. "_modified"`)
+	result, mods, matches, err := APIAdaptor(content, `<name>([A-Za-z]+)</name>`, `s1 = s1 .. "_modified"`)
 
 	assert.NoError(t, err, "Error processing content: %v", err)
 	assert.Equal(t, 2, matches, "Expected 2 matches, got %d", matches)
@@ -206,7 +205,7 @@ func TestStringUpperCase(t *testing.T) {
     <user>MARY</user>
 </users>`
 
-	result, mods, matches, err := ApiAdaptor(content, `<user>([A-Za-z]+)</user>`, `s1 = string.upper(s1)`)
+	result, mods, matches, err := APIAdaptor(content, `<user>([A-Za-z]+)</user>`, `s1 = string.upper(s1)`)
 
 	assert.NoError(t, err, "Error processing content: %v", err)
 	assert.Equal(t, 2, matches, "Expected 2 matches, got %d", matches)
@@ -225,7 +224,7 @@ func TestStringConcatenation(t *testing.T) {
     <product>Banana_fruit</product>
 </products>`
 
-	result, mods, matches, err := ApiAdaptor(content, `<product>([A-Za-z]+)</product>`, `s1 = s1 .. "_fruit"`)
+	result, mods, matches, err := APIAdaptor(content, `<product>([A-Za-z]+)</product>`, `s1 = s1 .. "_fruit"`)
 
 	assert.NoError(t, err, "Error processing content: %v", err)
 	assert.Equal(t, 2, matches, "Expected 2 matches, got %d", matches)
@@ -253,9 +252,9 @@ func TestDecimalValues(t *testing.T) {
 	`
 
 	regex := regexp.MustCompile(`(?s)<value>([0-9.]+)</value>.*?<multiplier>([0-9.]+)</multiplier>`)
-	luaExpr := BuildLuaScript("v1 = v1 * v2")
+	luaExpr := BuildLuaScript("v1 = v1 * v2", "")
 
-	result, _, _, err := ApiAdaptor(content, regex.String(), luaExpr)
+	result, _, _, err := APIAdaptor(content, regex.String(), luaExpr)
 	assert.NoError(t, err, "Error processing content: %v", err)
 
 	normalizedModified := normalizeWhitespace(result)
@@ -281,9 +280,9 @@ func TestLuaMathFunctions(t *testing.T) {
 	`
 
 	regex := regexp.MustCompile(`(?s)<value>(\d+)</value>`)
-	luaExpr := BuildLuaScript("v1 = math.sqrt(v1)")
+	luaExpr := BuildLuaScript("v1 = math.sqrt(v1)", "")
 
-	modifiedContent, _, _, err := ApiAdaptor(content, regex.String(), luaExpr)
+	modifiedContent, _, _, err := APIAdaptor(content, regex.String(), luaExpr)
 	assert.NoError(t, err, "Error processing content: %v", err)
 
 	normalizedModified := normalizeWhitespace(modifiedContent)
@@ -309,9 +308,9 @@ func TestDirectAssignment(t *testing.T) {
 	`
 
 	regex := regexp.MustCompile(`(?s)<value>(\d+)</value>`)
-	luaExpr := BuildLuaScript("=0")
+	luaExpr := BuildLuaScript("=0", "")
 
-	modifiedContent, _, _, err := ApiAdaptor(content, regex.String(), luaExpr)
+	modifiedContent, _, _, err := APIAdaptor(content, regex.String(), luaExpr)
 	assert.NoError(t, err, "Error processing content: %v", err)
 
 	normalizedModified := normalizeWhitespace(modifiedContent)
@@ -367,10 +366,10 @@ func TestStringAndNumericOperations(t *testing.T) {
 		t.Run(tt.name, func(t *testing.T) {
 			// Compile the regex pattern with multiline support
 			pattern := "(?s)" + tt.regexPattern
-			luaExpr := BuildLuaScript(tt.luaExpression)
+			luaExpr := BuildLuaScript(tt.luaExpression, "")
 
 			// Process with our function
-			result, modCount, _, err := ApiAdaptor(tt.input, pattern, luaExpr)
+			result, modCount, _, err := APIAdaptor(tt.input, pattern, luaExpr)
 			assert.NoError(t, err, "Process function failed: %v", err)
 
 			// Check results
@@ -428,10 +427,10 @@ func TestEdgeCases(t *testing.T) {
 		t.Run(tt.name, func(t *testing.T) {
 			// Make sure the regex can match across multiple lines
 			pattern := "(?s)" + tt.regexPattern
-			luaExpr := BuildLuaScript(tt.luaExpression)
+			luaExpr := BuildLuaScript(tt.luaExpression, "")
 
 			// Process with our function
-			result, modCount, _, err := ApiAdaptor(tt.input, pattern, luaExpr)
+			result, modCount, _, err := APIAdaptor(tt.input, pattern, luaExpr)
 			assert.NoError(t, err, "Process function failed: %v", err)
 
 			// Check results
@@ -454,7 +453,7 @@ func TestNamedCaptureGroups(t *testing.T) {
     </item>
 </config>`
 
-	result, mods, matches, err := ApiAdaptor(content, `(?s)<value>(?<amount>\d+)</value>`, "amount = amount * 2")
+	result, mods, matches, err := APIAdaptor(content, `(?s)<value>(?<amount>\d+)</value>`, "amount = amount * 2")
 
 	assert.NoError(t, err, "Error processing content: %v", err)
 	assert.Equal(t, 1, matches, "Expected 1 match, got %d", matches)
@@ -475,7 +474,7 @@ func TestNamedCaptureGroupsNum(t *testing.T) {
     </item>
 </config>`
 
-	result, mods, matches, err := ApiAdaptor(content, `(?s)<value>(?<amount>!num)</value>`, "amount = amount * 2")
+	result, mods, matches, err := APIAdaptor(content, `(?s)<value>(?<amount>!num)</value>`, "amount = amount * 2")
 
 	assert.NoError(t, err, "Error processing content: %v", err)
 	assert.Equal(t, 1, matches, "Expected 1 match, got %d", matches)
@@ -496,7 +495,7 @@ func TestMultipleNamedCaptureGroups(t *testing.T) {
     <quantity>15</quantity>
 </product>`
 
-	result, mods, matches, err := ApiAdaptor(content,
+	result, mods, matches, err := APIAdaptor(content,
 		`(?s)<name>(?<prodName>[^<]+)</name>.*?<price>(?<prodPrice>\d+\.\d+)</price>.*?<quantity>(?<prodQty>\d+)</quantity>`,
 		`prodName = string.upper(prodName)
 		 prodPrice = round(prodPrice + 8, 2)
@@ -519,7 +518,7 @@ func TestMixedIndexedAndNamedCaptures(t *testing.T) {
     <data>VALUE</data>
 </entry>`
 
-	result, mods, matches, err := ApiAdaptor(content,
+	result, mods, matches, err := APIAdaptor(content,
 		`(?s)<id>(\d+)</id>.*?<data>(?<dataField>[^<]+)</data>`,
 		`v1 = v1 * 2
 		 dataField = string.upper(dataField)`)
@@ -551,7 +550,7 @@ func TestComplexNestedNamedCaptures(t *testing.T) {
 		</contact>
 	</person>`
 
-	result, mods, matches, err := ApiAdaptor(content,
+	result, mods, matches, err := APIAdaptor(content,
 		`(?s)<details>.*?<name>(?<fullName>[^<]+)</name>.*?<age>(?<age>\d+)</age>`,
 		`fullName = string.upper(fullName) .. " (" .. age .. ")"`)
 
@@ -572,7 +571,7 @@ func TestNamedCaptureWithVariableReadback(t *testing.T) {
     <mana>300</mana>
 </stats>`
 
-	result, mods, matches, err := ApiAdaptor(content,
+	result, mods, matches, err := APIAdaptor(content,
 		`(?s)<health>(?<hp>\d+)</health>.*?<mana>(?<mp>\d+)</mana>`,
 		`hp = hp * 1.5
 		 mp = mp * 1.5`)
@@ -588,7 +587,7 @@ func TestNamedCaptureWithSpecialCharsInName(t *testing.T) {
 
 	expected := `<data value="84" min="10" max="100" />`
 
-	result, mods, matches, err := ApiAdaptor(content,
+	result, mods, matches, err := APIAdaptor(content,
 		`<data value="(?<val_1>\d+)"`,
 		`val_1 = val_1 * 2`)
 
@@ -603,7 +602,7 @@ func TestEmptyNamedCapture(t *testing.T) {
 
 	expected := `<tag attr="default" />`
 
-	result, mods, matches, err := ApiAdaptor(content,
+	result, mods, matches, err := APIAdaptor(content,
 		`attr="(?<value>.*?)"`,
 		`value = value == "" and "default" or value`)
 
@@ -618,7 +617,7 @@ func TestMultipleNamedCapturesInSameLine(t *testing.T) {
 
 	expected := `<rect x="20" y="40" width="200" height="100" />`
 
-	result, mods, matches, err := ApiAdaptor(content,
+	result, mods, matches, err := APIAdaptor(content,
 		`x="(?<x>\d+)" y="(?<y>\d+)" width="(?<w>\d+)" height="(?<h>\d+)"`,
 		`x = x * 2
 		 y = y * 2
@@ -642,7 +641,7 @@ func TestConditionalNamedCapture(t *testing.T) {
 	<item status="inactive" count="10" />
 	`
 
-	result, mods, matches, err := ApiAdaptor(content,
+	result, mods, matches, err := APIAdaptor(content,
 		`<item status="(?<status>[^"]+)" count="(?<count>\d+)"`,
 		`count = status == "active" and count * 2 or count`)
 
@@ -663,7 +662,7 @@ func TestLuaFunctionsOnNamedCaptures(t *testing.T) {
 	<user name="JANE SMITH" role="admin" />
 	`
 
-	result, mods, matches, err := ApiAdaptor(content,
+	result, mods, matches, err := APIAdaptor(content,
 		`<user name="(?<name>[^"]+)" role="(?<role>[^"]+)"`,
 		`-- Capitalize first letters for regular users
 		 if role == "user" then
@@ -693,7 +692,7 @@ func TestNamedCaptureWithMath(t *testing.T) {
 	<item price="19.99" quantity="3" total="59.97" />
 	`
 
-	result, mods, matches, err := ApiAdaptor(content,
+	result, mods, matches, err := APIAdaptor(content,
 		`<item price="(?<price>\d+\.\d+)" quantity="(?<qty>\d+)"!any$`,
 		`-- Calculate and add total
 		 replacement = string.format('<item price="%s" quantity="%s" total="%.2f" />',
@@ -713,7 +712,7 @@ func TestNamedCaptureWithGlobals(t *testing.T) {
 
 	expected := `<temp unit="F">77</temp>`
 
-	result, mods, matches, err := ApiAdaptor(content,
+	result, mods, matches, err := APIAdaptor(content,
 		`<temp unit="(?<unit>[CF]?)">(?<value>\d+)</temp>`,
 		`if unit == "C" then
 		  value = value * 9/5 + 32
@@ -740,7 +739,7 @@ func TestMixedDynamicAndNamedCaptures(t *testing.T) {
 	<color rgb="0,255,0" name="GREEN" hex="#00FF00" />
 	`
 
-	result, mods, matches, err := ApiAdaptor(content,
+	result, mods, matches, err := APIAdaptor(content,
 		`<color rgb="(?<r>\d+),(?<g>\d+),(?<b>\d+)" name="(?<colorName>[^"]+)" />`,
 		`-- Uppercase the name
 		 colorName = string.upper(colorName)
@@ -766,7 +765,7 @@ func TestNamedCapturesWithMultipleReferences(t *testing.T) {
 
 	expected := `<text format="uppercase" length="11">HELLO WORLD</text>`
 
-	result, mods, matches, err := ApiAdaptor(content,
+	result, mods, matches, err := APIAdaptor(content,
 		`<text>(?<content>[^<]+)</text>`,
 		`local uppercaseContent = string.upper(content)
 		 local contentLength = string.len(content)
@@ -784,7 +783,7 @@ func TestNamedCaptureWithJsonData(t *testing.T) {
 
 	expected := `<data>{"name":"JOHN","age":30}</data>`
 
-	result, mods, matches, err := ApiAdaptor(content,
+	result, mods, matches, err := APIAdaptor(content,
 		`<data>(?<json>\{.*?\})</data>`,
 		`-- Parse JSON (simplified, assumes valid JSON)
 		 local name = json:match('"name":"([^"]+)"')
@@ -814,7 +813,7 @@ func TestNamedCaptureInXML(t *testing.T) {
 	</product>
 	`
 
-	result, mods, matches, err := ApiAdaptor(content,
+	result, mods, matches, err := APIAdaptor(content,
 		`(?s)<price currency="(?<currency>[^"]+)">(?<price>\d+\.\d+)</price>.*?<stock>(?<stock>\d+)</stock>`,
 		`-- Add 20% to price if USD
 		 if currency == "USD" then
@@ -871,7 +870,7 @@ func TestComprehensiveNamedCaptures(t *testing.T) {
 	</products>
 	`
 
-	result, mods, matches, err := ApiAdaptor(content,
+	result, mods, matches, err := APIAdaptor(content,
 		`(?s)<product sku="(?<sku>[^"]+)" status="(?<status>[^"]+)"[^>]*>\s*<name>(?<product_name>[^<]+)</name>\s*<price currency="(?<currency>[^"]+)">(?<price>\d+\.\d+)</price>\s*<quantity>(?<qty>\d+)</quantity>`,
 		`-- Only process in-stock items
 		if status == "in-stock" then
@@ -925,7 +924,7 @@ func TestVariousNamedCaptureFormats(t *testing.T) {
 	</data>
 	`
 
-	result, mods, matches, err := ApiAdaptor(content,
+	result, mods, matches, err := APIAdaptor(content,
 		`<entry id="(?<id_num>\d+)" value="(?<val>\d+)"(?: status="(?<status>[^"]*)")? />`,
 		`-- Prefix the ID with "ID-"
 		id_num = "ID-" .. id_num
@@ -964,7 +963,7 @@ func TestSimpleNamedCapture(t *testing.T) {
 
 	expected := `<product name="WIDGET" price="19.99"/>`
 
-	result, mods, matches, err := ApiAdaptor(content,
+	result, mods, matches, err := APIAdaptor(content,
 		`name="(?<product_name>[^"]+)"`,
 		`product_name = string.upper(product_name)`)
 
@@ -979,29 +978,12 @@ func TestPatternWithoutPrefixGetsModified(t *testing.T) {
 	// Setup
 	pattern := "some.*pattern"
 
-	// Redirect stdout to capture fmt.Printf output
-	oldStdout := os.Stdout
-	r, w, _ := os.Pipe()
-	os.Stdout = w
-
 	// Execute function
 	result := resolveRegexPlaceholders(pattern)
 
-	// Restore stdout
-	w.Close()
-	os.Stdout = oldStdout
-
-	// Read captured output
-	var buf bytes.Buffer
-	io.Copy(&buf, r)
-	output := buf.String()
-
 	// Verify results
 	expectedPattern := "(?s)some.*pattern"
 	assert.Equal(t, expectedPattern, result, "Expected pattern to be %q, got %q", expectedPattern, result)
-
-	expectedOutput := fmt.Sprintf("Pattern modified to include (?s): %s\n", expectedPattern)
-	assert.Equal(t, expectedOutput, output, "Expected output message %q, got %q", expectedOutput, output)
 }
 
 // Empty string input returns "(?s)"
@@ -1009,29 +991,12 @@ func TestEmptyStringReturnsWithPrefix(t *testing.T) {
 	// Setup
 	pattern := ""
 
-	// Redirect stdout to capture fmt.Printf output
-	oldStdout := os.Stdout
-	r, w, _ := os.Pipe()
-	os.Stdout = w
-
 	// Execute function
 	result := resolveRegexPlaceholders(pattern)
 
-	// Restore stdout
-	w.Close()
-	os.Stdout = oldStdout
-
-	// Read captured output
-	var buf bytes.Buffer
-	io.Copy(&buf, r)
-	output := buf.String()
-
 	// Verify results
 	expectedPattern := "(?s)"
 	assert.Equal(t, expectedPattern, result, "Expected pattern to be %q, got %q", expectedPattern, result)
-
-	expectedOutput := fmt.Sprintf("Pattern modified to include (?s): %s\n", expectedPattern)
-	assert.Equal(t, expectedOutput, output, "Expected output message %q, got %q", expectedOutput, output)
 }
 
 // Named group with "!num" pattern gets replaced with proper regex for numbers

processor/surgical_json_test.go

@@ -0,0 +1,847 @@
+package processor
+
+import (
+	"cook/utils"
+	"testing"
+
+	"github.com/google/go-cmp/cmp"
+)
+
+func TestSurgicalJSONEditing(t *testing.T) {
+	tests := []struct {
+		name     string
+		content  string
+		luaCode  string
+		expected string
+	}{
+		{
+			name: "Modify single field",
+			content: `{
+  "name": "test",
+  "value": 42,
+  "description": "original"
+}`,
+			luaCode: `
+data.value = 84
+modified = true
+`,
+			expected: `{
+  "name": "test",
+  "value": 84,
+  "description": "original"
+}`,
+		},
+		{
+			name: "Add new field",
+			content: `{
+  "name": "test",
+  "value": 42
+}`,
+			luaCode: `
+data.newField = "added"
+modified = true
+`,
+			expected: `{
+  "name": "test",
+  "value": 42
+,"newField": "added"}`, // sjson.Set() adds new fields in compact format
+		},
+		{
+			name: "Modify nested field",
+			content: `{
+  "config": {
+    "settings": {
+      "enabled": false,
+      "timeout": 30
+    }
+  }
+}`,
+			luaCode: `
+data.config.settings.enabled = true
+data.config.settings.timeout = 60
+modified = true
+`,
+			expected: `{
+  "config": {
+    "settings": {
+      "enabled": true,
+      "timeout": 60
+    }
+  }
+}`,
+		},
+	}
+
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			command := utils.ModifyCommand{
+				Name: "test",
+				Lua:  tt.luaCode,
+			}
+
+			commands, err := ProcessJSON(tt.content, command, "test.json")
+			if err != nil {
+				t.Fatalf("ProcessJSON failed: %v", err)
+			}
+
+			if len(commands) == 0 {
+				t.Fatal("Expected at least one command")
+			}
+
+			// Apply the commands
+			result := tt.content
+			for _, cmd := range commands {
+				result = result[:cmd.From] + cmd.With + result[cmd.To:]
+			}
+
+			diff := cmp.Diff(result, tt.expected)
+			if diff != "" {
+				t.Errorf("Differences:\n%s", diff)
+			}
+
+			// Check the actual result matches expected
+			if result != tt.expected {
+				t.Errorf("Expected:\n%s\n\nGot:\n%s", tt.expected, result)
+			}
+		})
+	}
+}
+
+func TestSurgicalJSONPreservesFormatting(t *testing.T) {
+	// Test that surgical editing preserves the original formatting structure
+	content := `{
+  "Defaults": {
+    "Behaviour": "None",
+    "Description": "",
+    "DisplayName": "",
+    "FlavorText": "",
+    "Icon": "None",
+    "MaxStack": 1,
+    "Override_Glow_Icon": "None",
+    "Weight": 0,
+    "bAllowZeroWeight": false
+  },
+  "RowStruct": "/Script/Icarus.ItemableData",
+  "Rows": [
+    {
+      "Description": "NSLOCTEXT(\"D_Itemable\", \"Item_Fiber-Description\", \"A bundle of soft fiber, highly useful.\")",
+      "DisplayName": "NSLOCTEXT(\"D_Itemable\", \"Item_Fiber-DisplayName\", \"Fiber\")",
+      "FlavorText": "NSLOCTEXT(\"D_Itemable\", \"Item_Fiber-FlavorText\", \"Fiber is collected from bast, the strong inner bark of certain flowering plants.\")",
+      "Icon": "/Game/Assets/2DArt/UI/Items/Item_Icons/Resources/ITEM_Fibre.ITEM_Fibre",
+      "MaxStack": 1000000,
+      "Name": "Item_Fiber",
+      "Weight": 10
+    }
+  ]
+}`
+
+	expected := `{
+  "Defaults": {
+    "Behaviour": "None",
+    "Description": "",
+    "DisplayName": "",
+    "FlavorText": "",
+    "Icon": "None",
+    "MaxStack": 1,
+    "Override_Glow_Icon": "None",
+    "Weight": 0,
+    "bAllowZeroWeight": false
+  },
+  "RowStruct": "/Script/Icarus.ItemableData",
+  "Rows": [
+    {
+      "Description": "NSLOCTEXT(\"D_Itemable\", \"Item_Fiber-Description\", \"A bundle of soft fiber, highly useful.\")",
+      "DisplayName": "NSLOCTEXT(\"D_Itemable\", \"Item_Fiber-DisplayName\", \"Fiber\")",
+      "FlavorText": "NSLOCTEXT(\"D_Itemable\", \"Item_Fiber-FlavorText\", \"Fiber is collected from bast, the strong inner bark of certain flowering plants.\")",
+      "Icon": "/Game/Assets/2DArt/UI/Items/Item_Icons/Resources/ITEM_Fibre.ITEM_Fibre",
+      "MaxStack": 1000000,
+      "Name": "Item_Fiber",
+      "Weight": 500
+    }
+  ]
+}`
+
+	command := utils.ModifyCommand{
+		Name: "test",
+		Lua: `
+-- Modify the weight of the first item
+data.Rows[1].Weight = 500
+modified = true
+`,
+	}
+
+	commands, err := ProcessJSON(content, command, "test.json")
+	if err != nil {
+		t.Fatalf("ProcessJSON failed: %v", err)
+	}
+
+	if len(commands) == 0 {
+		t.Fatal("Expected at least one command")
+	}
+
+	// Apply the commands
+	result := content
+	for _, cmd := range commands {
+		result = result[:cmd.From] + cmd.With + result[cmd.To:]
+	}
+
+	diff := cmp.Diff(result, expected)
+	if diff != "" {
+		t.Errorf("Differences:\n%s", diff)
+	}
+
+	// Check that the result matches expected (preserves formatting and changes weight)
+	if result != expected {
+		t.Errorf("Expected:\n%s\n\nGot:\n%s", expected, result)
+	}
+}
+
+func TestSurgicalJSONPreservesFormatting2(t *testing.T) {
+	// Test that surgical editing preserves the original formatting structure
+	content := `
+{
+  "RowStruct": "/Script/Icarus.ProcessorRecipe",
+  "Defaults": {
+    "bForceDisableRecipe": false,
+    "Requirement": {
+      "RowName": "None",
+      "DataTableName": "D_Talents"
+    },
+    "SessionRequirement": {
+      "RowName": "None",
+      "DataTableName": "D_CharacterFlags"
+    },
+    "CharacterRequirement": {
+      "RowName": "None",
+      "DataTableName": "D_CharacterFlags"
+    },
+    "RequiredMillijoules": 2500,
+    "RecipeSets": [],
+    "ResourceCostMultipliers": [],
+    "Inputs": [
+      {
+        "Element": {
+          "RowName": "None",
+          "DataTableName": "D_ItemsStatic"
+        },
+        "Count": 1,
+        "DynamicProperties": []
+      }
+    ],
+    "Container": {
+      "Value": "None"
+    },
+    "ResourceInputs": [],
+    "bSelectOutputItemRandomly": false,
+    "bContainsContainer": false,
+    "ItemIconOverride": {
+      "ItemStaticData": {
+        "RowName": "None",
+        "DataTableName": "D_ItemsStatic"
+      },
+      "ItemDynamicData": [],
+      "ItemCustomStats": [],
+      "CustomProperties": {
+        "StaticWorldStats": [],
+        "StaticWorldHeldStats": [],
+        "Stats": [],
+        "Alterations": [],
+        "LivingItemSlots": []
+      },
+      "DatabaseGUID": "",
+      "ItemOwnerLookupId": -1,
+      "RuntimeTags": {
+        "GameplayTags": []
+      }
+    },
+    "Outputs": [
+      {
+        "Element": {
+          "RowName": "None",
+          "DataTableName": "D_ItemTemplate"
+        },
+        "Count": 1,
+        "DynamicProperties": []
+      }
+    ],
+    "ResourceOutputs": [],
+    "Refundable": "Inherit",
+    "ExperienceMultiplier": 1,
+    "Audio": {
+      "RowName": "None",
+      "DataTableName": "D_CraftingAudioData"
+    }
+  },
+  "Rows": [
+    {
+      "Name": "Biofuel1",
+      "RecipeSets": [
+        {
+          "RowName": "Composter",
+          "DataTableName": "D_RecipeSets"
+        }
+      ],
+      "Inputs": [
+        {
+          "Element": {
+            "RowName": "Raw_Meat",
+            "DataTableName": "D_ItemsStatic"
+          },
+          "Count": 2,
+          "DynamicProperties": []
+        },
+        {
+          "Element": {
+            "RowName": "Tree_Sap",
+            "DataTableName": "D_ItemsStatic"
+          },
+          "Count": 1,
+          "DynamicProperties": []
+        }
+      ],
+      "Outputs": [],
+      "Audio": {
+        "RowName": "Composter"
+      },
+      "ResourceOutputs": [
+        {
+          "Type": {
+            "Value": "Biofuel"
+          },
+          "RequiredUnits": 100
+        }
+      ]
+    }
+  ]
+}
+  `
+
+	expected := `
+{
+  "RowStruct": "/Script/Icarus.ProcessorRecipe",
+  "Defaults": {
+    "bForceDisableRecipe": false,
+    "Requirement": {
+      "RowName": "None",
+      "DataTableName": "D_Talents"
+    },
+    "SessionRequirement": {
+      "RowName": "None",
+      "DataTableName": "D_CharacterFlags"
+    },
+    "CharacterRequirement": {
+      "RowName": "None",
+      "DataTableName": "D_CharacterFlags"
+    },
+    "RequiredMillijoules": 2500,
+    "RecipeSets": [],
+    "ResourceCostMultipliers": [],
+    "Inputs": [
+      {
+        "Element": {
+          "RowName": "None",
+          "DataTableName": "D_ItemsStatic"
+        },
+        "Count": 1,
+        "DynamicProperties": []
+      }
+    ],
+    "Container": {
+      "Value": "None"
+    },
+    "ResourceInputs": [],
+    "bSelectOutputItemRandomly": false,
+    "bContainsContainer": false,
+    "ItemIconOverride": {
+      "ItemStaticData": {
+        "RowName": "None",
+        "DataTableName": "D_ItemsStatic"
+      },
+      "ItemDynamicData": [],
+      "ItemCustomStats": [],
+      "CustomProperties": {
+        "StaticWorldStats": [],
+        "StaticWorldHeldStats": [],
+        "Stats": [],
+        "Alterations": [],
+        "LivingItemSlots": []
+      },
+      "DatabaseGUID": "",
+      "ItemOwnerLookupId": -1,
+      "RuntimeTags": {
+        "GameplayTags": []
+      }
+    },
+    "Outputs": [
+      {
+        "Element": {
+          "RowName": "None",
+          "DataTableName": "D_ItemTemplate"
+        },
+        "Count": 1,
+        "DynamicProperties": []
+      }
+    ],
+    "ResourceOutputs": [],
+    "Refundable": "Inherit",
+    "ExperienceMultiplier": 1,
+    "Audio": {
+      "RowName": "None",
+      "DataTableName": "D_CraftingAudioData"
+    }
+  },
+  "Rows": [
+    {
+      "Name": "Biofuel1",
+      "RecipeSets": [
+        {
+          "RowName": "Composter",
+          "DataTableName": "D_RecipeSets"
+        }
+      ],
+      "Inputs": [
+        {
+          "Element": {
+            "RowName": "Raw_Meat",
+            "DataTableName": "D_ItemsStatic"
+          },
+          "Count": 2,
+          "DynamicProperties": []
+        }
+      ],
+      "Outputs": [],
+      "Audio": {
+        "RowName": "Composter"
+      },
+      "ResourceOutputs": [
+        {
+          "Type": {
+            "Value": "Biofuel"
+          },
+          "RequiredUnits": 100
+        }
+      ]
+    }
+  ]
+}
+  `
+
+	command := utils.ModifyCommand{
+		Name: "test",
+		Lua: `
+    -- Define regex patterns for matching recipe names
+    local function matchesPattern(name, pattern)
+      local matches = re(pattern, name)
+      -- Check if matches table has any content (index 0 or 1 should exist if there's a match)
+      return matches and (matches[0] or matches[1])
+    end
+
+    -- Selection pattern for recipes that get multiplied
+    local selectionPattern = "(?-s)(Bulk_)?(Pistol|Rifle).*?Round.*?|(Carbon|Composite)_Paste.*|(Gold|Copper)_Wire|(Ironw|Copper)_Nail|(Platinum|Steel|Cold_Steel|Titanium)_Ingot|.*?Shotgun_Shell.*?|.*_Arrow|.*_Bolt|.*_Fertilizer_?\\d*|.*_Grenade|.*_Pill|.*_Tonic|Aluminum|Ammo_Casing|Animal_Fat|Carbon_Fiber|Composites|Concrete_Mix|Cured_Leather_?\\d?|Electronics|Epoxy_?\\d?|Glass\\d?|Gunpowder\\w*|Health_.*|Titanium_Plate|Organic_Resin|Platinum_Sheath|Refined_[a-zA-Z]+|Rope|Shotgun_Casing|Steel_Bloom\\d?|Tree_Sap\\w*"
+
+    -- Ingot pattern for recipes that get count set to 1
+    local ingotPattern = "(?-s)(Platinum|Steel|Cold_Steel|Titanium)_Ingot|Aluminum|Refined_[a-zA-Z]+|Glass\\d?"
+
+    local factor = 16
+    local bonus = 0.5
+
+    for _, row in ipairs(data.Rows) do
+      local recipeName = row.Name
+
+      -- Special case: Biofuel recipes - remove Tree_Sap input
+      if string.find(recipeName, "Biofuel") then
+        if row.Inputs then
+          for i = #row.Inputs, 1, -1 do
+            local input = row.Inputs[i]
+            if input.Element and input.Element.RowName and string.find(input.Element.RowName, "Tree_Sap") then
+              table.remove(row.Inputs, i)
+              print("Removing input 'Tree_Sap' from processor recipe '" .. recipeName .. "'")
+            end
+          end
+        end
+      end
+
+      -- Ingot recipes: set input and output counts to 1
+      if matchesPattern(recipeName, ingotPattern) then
+        if row.Inputs then
+          for _, input in ipairs(row.Inputs) do
+            input.Count = 1
+          end
+        end
+        if row.Outputs then
+          for _, output in ipairs(row.Outputs) do
+            output.Count = 1
+          end
+        end
+      end
+
+      -- Selected recipes: multiply inputs by factor, outputs by factor * (1 + bonus)
+      if matchesPattern(recipeName, selectionPattern) then
+        if row.Inputs then
+          for _, input in ipairs(row.Inputs) do
+            local oldCount = input.Count
+            input.Count = input.Count * factor
+            print("Recipe " .. recipeName .. " Input.Count: " .. oldCount .. " -> " .. input.Count)
+          end
+        end
+
+        if row.Outputs then
+          for _, output in ipairs(row.Outputs) do
+            local oldCount = output.Count
+            output.Count = math.floor(output.Count * factor * (1 + bonus))
+            print("Recipe " .. recipeName .. " Output.Count: " .. oldCount .. " -> " .. output.Count)
+          end
+        end
+      end
+    end
+`,
+	}
+
+	commands, err := ProcessJSON(content, command, "test.json")
+	if err != nil {
+		t.Fatalf("ProcessJSON failed: %v", err)
+	}
+
+	if len(commands) == 0 {
+		t.Fatal("Expected at least one command")
+	}
+
+	// Apply the commands
+	result := content
+	for _, cmd := range commands {
+		result = result[:cmd.From] + cmd.With + result[cmd.To:]
+	}
+
+	diff := cmp.Diff(result, expected)
+	if diff != "" {
+		t.Errorf("Differences:\n%s", diff)
+	}
+
+	// Check that the result matches expected (preserves formatting and changes weight)
+	if result != expected {
+		t.Errorf("Expected:\n%s\n\nGot:\n%s", expected, result)
+	}
+}
+
+func TestRetardedJSONEditing(t *testing.T) {
+	original := `{
+  "RowStruct": "/Script/Icarus.ItemableData",
+  "Defaults": {
+    "Behaviour": "None",
+    "DisplayName": "",
+    "Icon": "None",
+    "Override_Glow_Icon": "None",
+    "Description": "",
+    "FlavorText": "",
+    "Weight": 0,
+    "bAllowZeroWeight": false,
+    "MaxStack": 1
+  },
+  "Rows": [
+		{
+      "DisplayName": "NSLOCTEXT(\"D_Itemable\", \"Item_Fiber-DisplayName\", \"Fiber\")",
+      "Icon": "/Game/Assets/2DArt/UI/Items/Item_Icons/Resources/ITEM_Fibre.ITEM_Fibre",
+      "Description": "NSLOCTEXT(\"D_Itemable\", \"Item_Fiber-Description\", \"A bundle of soft fiber, highly useful.\")",
+      "FlavorText": "NSLOCTEXT(\"D_Itemable\", \"Item_Fiber-FlavorText\", \"Fiber is collected from bast, the strong inner bark of certain flowering plants.\")",
+      "Weight": 10,
+      "MaxStack": 200,
+      "Name": "Item_Fiber"
+    }
+	]
+}`
+
+	expected := `{
+  "RowStruct": "/Script/Icarus.ItemableData",
+  "Defaults": {
+    "Behaviour": "None",
+    "DisplayName": "",
+    "Icon": "None",
+    "Override_Glow_Icon": "None",
+    "Description": "",
+    "FlavorText": "",
+    "Weight": 0,
+    "bAllowZeroWeight": false,
+    "MaxStack": 1
+  },
+  "Rows": [
+		{
+      "DisplayName": "NSLOCTEXT(\"D_Itemable\", \"Item_Fiber-DisplayName\", \"Fiber\")",
+      "Icon": "/Game/Assets/2DArt/UI/Items/Item_Icons/Resources/ITEM_Fibre.ITEM_Fibre",
+      "Description": "NSLOCTEXT(\"D_Itemable\", \"Item_Fiber-Description\", \"A bundle of soft fiber, highly useful.\")",
+      "FlavorText": "NSLOCTEXT(\"D_Itemable\", \"Item_Fiber-FlavorText\", \"Fiber is collected from bast, the strong inner bark of certain flowering plants.\")",
+      "Weight": 10,
+      "MaxStack": 1000000,
+      "Name": "Item_Fiber"
+    }
+	]
+}`
+
+	command := utils.ModifyCommand{
+		Name: "test",
+		Lua: `
+    for _, row in ipairs(data.Rows) do
+      if row.MaxStack then
+        if string.find(row.Name, "Carrot") or string.find(row.Name, "Potato") then
+          row.MaxStack = 25
+        else
+          row.MaxStack = row.MaxStack * 10000
+          if row.MaxStack > 1000000 then
+            row.MaxStack = 1000000
+          end
+        end
+      end
+    end
+`,
+	}
+
+	commands, err := ProcessJSON(original, command, "test.json")
+	if err != nil {
+		t.Fatalf("ProcessJSON failed: %v", err)
+	}
+
+	if len(commands) == 0 {
+		t.Fatal("Expected at least one command")
+	}
+
+	// Apply the commands
+	result := original
+	for _, cmd := range commands {
+		result = result[:cmd.From] + cmd.With + result[cmd.To:]
+	}
+
+	diff := cmp.Diff(result, expected)
+	if diff != "" {
+		t.Errorf("Differences:\n%s", diff)
+	}
+
+	// Check that the weight was changed
+	if result != expected {
+		t.Errorf("Expected:\n%s\nGot:\n%s", expected, result)
+	}
+}
+
+func TestRetardedJSONEditing2(t *testing.T) {
+	original := `
+  {
+      "Rows": [
+        {
+            "Name": "Deep_Mining_Drill_Biofuel",
+            "Meshable": {
+                "RowName": "Mesh_Deep_Mining_Drill_Biofuel"
+            },
+            "Itemable": {
+                "RowName": "Item_Deep_Mining_Drill_Biofuel"
+            },
+            "Interactable": {
+                "RowName": "Deployable"
+            },
+            "Focusable": {
+                "RowName": "Focusable_1H"
+            },
+            "Highlightable": {
+                "RowName": "Generic"
+            },
+            "Actionable": {
+                "RowName": "Deployable"
+            },
+            "Usable": {
+                "RowName": "Place"
+            },
+            "Deployable": {
+                "RowName": "Deep_Mining_Drill_Biofuel"
+            },
+            "Durable": {
+                "RowName": "Deployable_750"
+            },
+            "Inventory": {
+                "RowName": "Deep_Mining_Drill_Biofuel"
+            },
+            "Decayable": {
+                "RowName": "Decay_MetaItem"
+            },
+            "Generator": {
+                "RowName": "Deep_Mining_Biofuel_Drill"
+            },
+            "Resource": {
+                "RowName": "Simple_Internal_Flow_Only"
+            },
+            "Manual_Tags": {
+                "GameplayTags": [
+                    {
+                        "TagName": "Item.Machine"
+                    }
+                ]
+            },
+            "Generated_Tags": {
+                "GameplayTags": [
+                    {
+                        "TagName": "Item.Machine"
+                    },
+                    {
+                        "TagName": "Traits.Meshable"
+                    },
+                    {
+                        "TagName": "Traits.Itemable"
+                    },
+                    {
+                        "TagName": "Traits.Interactable"
+                    },
+                    {
+                        "TagName": "Traits.Highlightable"
+                    },
+                    {
+                        "TagName": "Traits.Actionable"
+                    },
+                    {
+                        "TagName": "Traits.Usable"
+                    },
+                    {
+                        "TagName": "Traits.Deployable"
+                    },
+                    {
+                        "TagName": "Traits.Durable"
+                    },
+                    {
+                        "TagName": "Traits.Inventory"
+                    }
+                ],
+                "ParentTags": []
+            }
+        }
+      ]
+  }
+  `
+
+	expected := `
+  {
+      "Rows": [
+        {
+            "Name": "Deep_Mining_Drill_Biofuel",
+            "Meshable": {
+                "RowName": "Mesh_Deep_Mining_Drill_Biofuel"
+            },
+            "Itemable": {
+                "RowName": "Item_Deep_Mining_Drill_Biofuel"
+            },
+            "Interactable": {
+                "RowName": "Deployable"
+            },
+            "Focusable": {
+                "RowName": "Focusable_1H"
+            },
+            "Highlightable": {
+                "RowName": "Generic"
+            },
+            "Actionable": {
+                "RowName": "Deployable"
+            },
+            "Usable": {
+                "RowName": "Place"
+            },
+            "Deployable": {
+                "RowName": "Deep_Mining_Drill_Biofuel"
+            },
+            "Durable": {
+                "RowName": "Deployable_750"
+            },
+            "Inventory": {
+                "RowName": "Deep_Mining_Drill_Biofuel"
+            },
+            "Decayable": {
+                "RowName": "Decay_MetaItem"
+            },
+            "Generator": {
+                "RowName": "Deep_Mining_Biofuel_Drill"
+            },
+            "Resource": {
+                "RowName": "Simple_Internal_Flow_Only"
+            },
+            "Manual_Tags": {
+                "GameplayTags": [
+                    {
+                        "TagName": "Item.Machine"
+                    }
+                ]
+            },
+            "Generated_Tags": {
+                "GameplayTags": [
+                    {
+                        "TagName": "Item.Machine"
+                    },
+                    {
+                        "TagName": "Traits.Meshable"
+                    },
+                    {
+                        "TagName": "Traits.Itemable"
+                    },
+                    {
+                        "TagName": "Traits.Interactable"
+                    },
+                    {
+                        "TagName": "Traits.Highlightable"
+                    },
+                    {
+                        "TagName": "Traits.Actionable"
+                    },
+                    {
+                        "TagName": "Traits.Usable"
+                    },
+                    {
+                        "TagName": "Traits.Deployable"
+                    },
+                    {
+                        "TagName": "Traits.Durable"
+                    },
+                    {
+                        "TagName": "Traits.Inventory"
+                    }
+                ],
+                "ParentTags": []
+            }
+        ,"AdditionalStats": {"(Value=\"BaseDeepMiningDrillSpeed_+%\")":4000}}
+      ]
+  }
+  `
+
+	command := utils.ModifyCommand{
+		Name: "test",
+		Lua: `
+    for i, row in ipairs(data.Rows) do
+      -- Special case: Deep_Mining_Drill_Biofuel
+      if string.find(row.Name, "Deep_Mining_Drill_Biofuel") then
+        print("[DEBUG]  Special case: Deep_Mining_Drill_Biofuel")
+        if not row.AdditionalStats then
+          print("[DEBUG]   Creating AdditionalStats table for Deep_Mining_Drill_Biofuel")
+          row.AdditionalStats = {}
+        end
+        print("[DEBUG]   Setting BaseDeepMiningDrillSpeed_+% to 4000")
+        row.AdditionalStats["(Value=\\\"BaseDeepMiningDrillSpeed_+%\\\")"] = 4000
+      end
+    end
+`,
+	}
+
+	commands, err := ProcessJSON(original, command, "test.json")
+	if err != nil {
+		t.Fatalf("ProcessJSON failed: %v", err)
+	}
+
+	if len(commands) == 0 {
+		t.Fatal("Expected at least one command")
+	}
+
+	// Apply the commands
+	result := original
+	for _, cmd := range commands {
+		result = result[:cmd.From] + cmd.With + result[cmd.To:]
+	}
+
+	diff := cmp.Diff(result, expected)
+	if diff != "" {
+		t.Errorf("Differences:\n%s", diff)
+	}
+
+	if result != expected {
+		t.Errorf("Expected:\n%s\nGot:\n%s", expected, result)
+	}
+}

processor/test_helper.go

@@ -1,26 +0,0 @@
-package processor
-
-import (
-	"io"
-	"modify/logger"
-	"os"
-)
-
-func init() {
-	// Only modify logger in test mode
-	// This checks if we're running under 'go test'
-	if os.Getenv("GO_TESTING") == "1" || os.Getenv("TESTING") == "1" {
-		// Initialize logger with ERROR level for tests
-		// to minimize noise in test output
-		logger.Init(logger.LevelError)
-
-		// Optionally redirect logger output to discard
-		// This prevents logger output from interfering with test output
-		disableTestLogs := os.Getenv("ENABLE_TEST_LOGS") != "1"
-		if disableTestLogs {
-			// Create a new logger that writes to nowhere
-			silentLogger := logger.New(io.Discard, "", 0)
-			logger.DefaultLogger = silentLogger
-		}
-	}
-}

processor/xml.go

@@ -0,0 +1,533 @@
+package processor
+
+import (
+	"cook/utils"
+	"encoding/xml"
+	"fmt"
+	"io"
+	"sort"
+	"strconv"
+	"strings"
+
+	logger "git.site.quack-lab.dev/dave/cylogger"
+	lua "github.com/yuin/gopher-lua"
+)
+
+var xmlLogger = logger.Default.WithPrefix("processor/xml")
+
+// XMLElement represents a parsed XML element with position tracking
+type XMLElement struct {
+	Tag        string
+	Attributes map[string]XMLAttribute
+	Text       string
+	Children   []*XMLElement
+	StartPos   int64
+	EndPos     int64
+	TextStart  int64
+	TextEnd    int64
+}
+
+// XMLAttribute represents an attribute with its position in the source
+type XMLAttribute struct {
+	Value      string
+	ValueStart int64
+	ValueEnd   int64
+}
+
+// parseXMLWithPositions parses XML while tracking byte positions of all elements and attributes
+func parseXMLWithPositions(content string) (*XMLElement, error) {
+	decoder := xml.NewDecoder(strings.NewReader(content))
+	var root *XMLElement
+	var stack []*XMLElement
+	var lastPos int64
+
+	for {
+		token, err := decoder.Token()
+		if err == io.EOF {
+			break
+		}
+		if err != nil {
+			return nil, fmt.Errorf("failed to parse XML: %v", err)
+		}
+
+		offset := decoder.InputOffset()
+
+		switch t := token.(type) {
+		case xml.StartElement:
+			// Find the actual start position of this element by searching for "<tagname"
+			tagSearchPattern := "<" + t.Name.Local
+			startPos := int64(strings.LastIndex(content[:offset], tagSearchPattern))
+
+			element := &XMLElement{
+				Tag:        t.Name.Local,
+				Attributes: make(map[string]XMLAttribute),
+				StartPos:   startPos,
+				Children:   []*XMLElement{},
+			}
+
+			// Parse attributes - search within the tag boundaries
+			if len(t.Attr) > 0 {
+				tagEnd := offset
+				tagSection := content[startPos:tagEnd]
+
+				for _, attr := range t.Attr {
+					// Find attribute in the tag section: attrname="value"
+					attrPattern := attr.Name.Local + `="`
+					attrIdx := strings.Index(tagSection, attrPattern)
+					if attrIdx >= 0 {
+						valueStart := startPos + int64(attrIdx) + int64(len(attrPattern))
+						valueEnd := valueStart + int64(len(attr.Value))
+						element.Attributes[attr.Name.Local] = XMLAttribute{
+							Value:      attr.Value,
+							ValueStart: valueStart,
+							ValueEnd:   valueEnd,
+						}
+					}
+				}
+			}
+
+			if len(stack) > 0 {
+				parent := stack[len(stack)-1]
+				parent.Children = append(parent.Children, element)
+			} else {
+				root = element
+			}
+
+			stack = append(stack, element)
+			lastPos = offset
+
+		case xml.CharData:
+			rawText := string(t)
+			text := strings.TrimSpace(rawText)
+			if len(stack) > 0 && text != "" {
+				current := stack[len(stack)-1]
+				current.Text = text
+
+				// The text content is between lastPos (after >) and offset (before </)
+				// Search for the trimmed text within the raw content
+				textInContent := content[lastPos:offset]
+				trimmedStart := strings.Index(textInContent, text)
+				if trimmedStart >= 0 {
+					current.TextStart = lastPos + int64(trimmedStart)
+					current.TextEnd = current.TextStart + int64(len(text))
+				}
+			}
+			lastPos = offset
+
+		case xml.EndElement:
+			if len(stack) > 0 {
+				current := stack[len(stack)-1]
+				current.EndPos = offset
+				stack = stack[:len(stack)-1]
+			}
+			lastPos = offset
+		}
+	}
+
+	return root, nil
+}
+
+// XMLChange represents a detected difference between original and modified XML structures
+type XMLChange struct {
+	Type       string // "text", "attribute", "add_element", "remove_element"
+	Path       string
+	OldValue   string
+	NewValue   string
+	StartPos   int64
+	EndPos     int64
+	InsertText string
+}
+
+func findXMLChanges(original, modified *XMLElement, path string) []XMLChange {
+	var changes []XMLChange
+
+	// Check text content changes
+	if original.Text != modified.Text {
+		changes = append(changes, XMLChange{
+			Type:     "text",
+			Path:     path,
+			OldValue: original.Text,
+			NewValue: modified.Text,
+			StartPos: original.TextStart,
+			EndPos:   original.TextEnd,
+		})
+	}
+
+	// Check attribute changes
+	for attrName, origAttr := range original.Attributes {
+		if modAttr, exists := modified.Attributes[attrName]; exists {
+			if origAttr.Value != modAttr.Value {
+				changes = append(changes, XMLChange{
+					Type:     "attribute",
+					Path:     path + "/@" + attrName,
+					OldValue: origAttr.Value,
+					NewValue: modAttr.Value,
+					StartPos: origAttr.ValueStart,
+					EndPos:   origAttr.ValueEnd,
+				})
+			}
+		} else {
+			// Attribute removed
+			changes = append(changes, XMLChange{
+				Type:     "remove_attribute",
+				Path:     path + "/@" + attrName,
+				OldValue: origAttr.Value,
+				StartPos: origAttr.ValueStart - int64(len(attrName)+2), // Include attr=" part
+				EndPos:   origAttr.ValueEnd + 1,                        // Include closing "
+			})
+		}
+	}
+
+	// Check for added attributes
+	for attrName, modAttr := range modified.Attributes {
+		if _, exists := original.Attributes[attrName]; !exists {
+			changes = append(changes, XMLChange{
+				Type:       "add_attribute",
+				Path:       path + "/@" + attrName,
+				NewValue:   modAttr.Value,
+				StartPos:   original.StartPos, // Will be adjusted to insert after tag name
+				InsertText: fmt.Sprintf(` %s="%s"`, attrName, modAttr.Value),
+			})
+		}
+	}
+
+	// Check children recursively
+	origChildMap := make(map[string][]*XMLElement)
+	for _, child := range original.Children {
+		origChildMap[child.Tag] = append(origChildMap[child.Tag], child)
+	}
+
+	modChildMap := make(map[string][]*XMLElement)
+	for _, child := range modified.Children {
+		modChildMap[child.Tag] = append(modChildMap[child.Tag], child)
+	}
+
+	// Compare children by tag name
+	processedTags := make(map[string]bool)
+
+	for tag, origChildren := range origChildMap {
+		processedTags[tag] = true
+		modChildren := modChildMap[tag]
+
+		// Match children by index
+		maxLen := len(origChildren)
+		if len(modChildren) > maxLen {
+			maxLen = len(modChildren)
+		}
+
+		for i := 0; i < maxLen; i++ {
+			childPath := fmt.Sprintf("%s/%s[%d]", path, tag, i)
+			if i < len(origChildren) && i < len(modChildren) {
+				// Both exist, compare recursively
+				childChanges := findXMLChanges(origChildren[i], modChildren[i], childPath)
+				changes = append(changes, childChanges...)
+			} else if i < len(origChildren) {
+				// Child removed
+				changes = append(changes, XMLChange{
+					Type:     "remove_element",
+					Path:     childPath,
+					StartPos: origChildren[i].StartPos,
+					EndPos:   origChildren[i].EndPos,
+				})
+			}
+		}
+
+		// Handle added children
+		if len(modChildren) > len(origChildren) {
+			for i := len(origChildren); i < len(modChildren); i++ {
+				childPath := fmt.Sprintf("%s/%s[%d]", path, tag, i)
+				// Generate XML text for the new element
+				xmlText := serializeXMLElement(modChildren[i], "  ")
+				changes = append(changes, XMLChange{
+					Type:       "add_element",
+					Path:       childPath,
+					InsertText: xmlText,
+					StartPos:   original.EndPos - int64(len(original.Tag)+3), // Before closing tag
+				})
+			}
+		}
+	}
+
+	return changes
+}
+
+// serializeXMLElement converts an XMLElement back to XML text
+func serializeXMLElement(elem *XMLElement, indent string) string {
+	var sb strings.Builder
+	sb.WriteString(indent)
+	sb.WriteString("<")
+	sb.WriteString(elem.Tag)
+
+	// Write attributes
+	attrNames := make([]string, 0, len(elem.Attributes))
+	for name := range elem.Attributes {
+		attrNames = append(attrNames, name)
+	}
+	sort.Strings(attrNames)
+
+	for _, name := range attrNames {
+		attr := elem.Attributes[name]
+		sb.WriteString(fmt.Sprintf(` %s="%s"`, name, attr.Value))
+	}
+
+	if elem.Text == "" && len(elem.Children) == 0 {
+		sb.WriteString(" />")
+		return sb.String()
+	}
+
+	sb.WriteString(">")
+
+	if elem.Text != "" {
+		sb.WriteString(elem.Text)
+	}
+
+	if len(elem.Children) > 0 {
+		sb.WriteString("\n")
+		for _, child := range elem.Children {
+			sb.WriteString(serializeXMLElement(child, indent+"  "))
+			sb.WriteString("\n")
+		}
+		sb.WriteString(indent)
+	}
+
+	sb.WriteString("</")
+	sb.WriteString(elem.Tag)
+	sb.WriteString(">")
+
+	return sb.String()
+}
+
+// applyXMLChanges generates ReplaceCommands from detected XML changes
+func applyXMLChanges(changes []XMLChange) []utils.ReplaceCommand {
+	var commands []utils.ReplaceCommand
+
+	for _, change := range changes {
+		switch change.Type {
+		case "text":
+			commands = append(commands, utils.ReplaceCommand{
+				From: int(change.StartPos),
+				To:   int(change.EndPos),
+				With: change.NewValue,
+			})
+
+		case "attribute":
+			commands = append(commands, utils.ReplaceCommand{
+				From: int(change.StartPos),
+				To:   int(change.EndPos),
+				With: change.NewValue,
+			})
+
+		case "add_attribute":
+			// Insert after tag name, before > or />
+			commands = append(commands, utils.ReplaceCommand{
+				From: int(change.StartPos),
+				To:   int(change.StartPos),
+				With: change.InsertText,
+			})
+
+		case "remove_attribute":
+			commands = append(commands, utils.ReplaceCommand{
+				From: int(change.StartPos),
+				To:   int(change.EndPos),
+				With: "",
+			})
+
+		case "add_element":
+			commands = append(commands, utils.ReplaceCommand{
+				From: int(change.StartPos),
+				To:   int(change.StartPos),
+				With: "\n" + change.InsertText,
+			})
+
+		case "remove_element":
+			commands = append(commands, utils.ReplaceCommand{
+				From: int(change.StartPos),
+				To:   int(change.EndPos),
+				With: "",
+			})
+		}
+	}
+
+	return commands
+}
+
+// deepCopyXMLElement creates a deep copy of an XMLElement
+func deepCopyXMLElement(elem *XMLElement) *XMLElement {
+	if elem == nil {
+		return nil
+	}
+
+	copied := &XMLElement{
+		Tag:        elem.Tag,
+		Text:       elem.Text,
+		StartPos:   elem.StartPos,
+		EndPos:     elem.EndPos,
+		TextStart:  elem.TextStart,
+		TextEnd:    elem.TextEnd,
+		Attributes: make(map[string]XMLAttribute),
+		Children:   make([]*XMLElement, len(elem.Children)),
+	}
+
+	for k, v := range elem.Attributes {
+		copied.Attributes[k] = v
+	}
+
+	for i, child := range elem.Children {
+		copied.Children[i] = deepCopyXMLElement(child)
+	}
+
+	return copied
+}
+
+// Helper function to parse numeric values
+func parseNumeric(s string) (float64, bool) {
+	if f, err := strconv.ParseFloat(s, 64); err == nil {
+		return f, true
+	}
+	return 0, false
+}
+
+// Helper function to format numeric values
+func formatNumeric(f float64) string {
+	if f == float64(int64(f)) {
+		return strconv.FormatInt(int64(f), 10)
+	}
+	return strconv.FormatFloat(f, 'f', -1, 64)
+}
+
+// ProcessXML applies Lua processing to XML content with surgical editing
+func ProcessXML(content string, command utils.ModifyCommand, filename string) ([]utils.ReplaceCommand, error) {
+	processXMLLogger := xmlLogger.WithPrefix("ProcessXML").WithField("commandName", command.Name).WithField("file", filename)
+	processXMLLogger.Debug("Starting XML processing for file")
+
+	// Parse XML with position tracking
+	originalElem, err := parseXMLWithPositions(content)
+	if err != nil {
+		processXMLLogger.Error("Failed to parse XML: %v", err)
+		return nil, fmt.Errorf("failed to parse XML: %v", err)
+	}
+	processXMLLogger.Debug("Successfully parsed XML content")
+
+	// Create Lua state
+	L, err := NewLuaState()
+	if err != nil {
+		processXMLLogger.Error("Error creating Lua state: %v", err)
+		return nil, fmt.Errorf("error creating Lua state: %v", err)
+	}
+	defer L.Close()
+
+	// Set filename global
+	L.SetGlobal("file", lua.LString(filename))
+
+	// Create modifiable copy
+	modifiedElem := deepCopyXMLElement(originalElem)
+
+	// Convert to Lua table and set as global
+	luaTable := xmlElementToLuaTable(L, modifiedElem)
+	L.SetGlobal("root", luaTable)
+	processXMLLogger.Debug("Set XML data as Lua global 'root'")
+
+	// Build and execute Lua script
+	luaExpr := BuildJSONLuaScript(command.Lua, command.SourceDir) // Reuse JSON script builder
+	processXMLLogger.Debug("Built Lua script from expression: %q", command.Lua)
+
+	if err := L.DoString(luaExpr); err != nil {
+		processXMLLogger.Error("Lua script execution failed: %v\nScript: %s", err, luaExpr)
+		return nil, fmt.Errorf("lua script execution failed: %v", err)
+	}
+	processXMLLogger.Debug("Lua script executed successfully")
+
+	// Check if modification flag is set
+	modifiedVal := L.GetGlobal("modified")
+	if modifiedVal.Type() != lua.LTBool || !lua.LVAsBool(modifiedVal) {
+		processXMLLogger.Debug("Skipping - no modifications indicated by Lua script")
+		return nil, nil
+	}
+
+	// Get the modified data back from Lua
+	modifiedTable := L.GetGlobal("root")
+	if modifiedTable.Type() != lua.LTTable {
+		processXMLLogger.Error("Expected 'root' to be a table after Lua processing")
+		return nil, fmt.Errorf("expected 'root' to be a table after Lua processing")
+	}
+
+	// Apply Lua modifications back to XMLElement
+	luaTableToXMLElement(L, modifiedTable.(*lua.LTable), modifiedElem)
+
+	// Find changes between original and modified
+	changes := findXMLChanges(originalElem, modifiedElem, "")
+	processXMLLogger.Debug("Found %d changes", len(changes))
+
+	if len(changes) == 0 {
+		return nil, nil
+	}
+
+	// Generate surgical replace commands
+	commands := applyXMLChanges(changes)
+	processXMLLogger.Debug("Generated %d replace commands", len(commands))
+
+	return commands, nil
+}
+
+// xmlElementToLuaTable converts an XMLElement to a Lua table
+func xmlElementToLuaTable(L *lua.LState, elem *XMLElement) *lua.LTable {
+	table := L.CreateTable(0, 4)
+	table.RawSetString("_tag", lua.LString(elem.Tag))
+
+	if len(elem.Attributes) > 0 {
+		attrs := L.CreateTable(0, len(elem.Attributes))
+		for name, attr := range elem.Attributes {
+			attrs.RawSetString(name, lua.LString(attr.Value))
+		}
+		table.RawSetString("_attr", attrs)
+	}
+
+	if len(elem.Children) > 0 {
+		children := L.CreateTable(len(elem.Children), 0)
+		for i, child := range elem.Children {
+			children.RawSetInt(i+1, xmlElementToLuaTable(L, child))
+		}
+		table.RawSetString("_children", children)
+	}
+
+	return table
+}
+
+// luaTableToXMLElement applies Lua table modifications back to XMLElement
+func luaTableToXMLElement(L *lua.LState, table *lua.LTable, elem *XMLElement) {
+	// Update attributes
+	if attrVal := table.RawGetString("_attr"); attrVal.Type() == lua.LTTable {
+		attrTable := attrVal.(*lua.LTable)
+		// Clear and rebuild attributes
+		elem.Attributes = make(map[string]XMLAttribute)
+		attrTable.ForEach(func(key lua.LValue, value lua.LValue) {
+			if key.Type() == lua.LTString && value.Type() == lua.LTString {
+				attrName := string(key.(lua.LString))
+				attrValue := string(value.(lua.LString))
+				elem.Attributes[attrName] = XMLAttribute{Value: attrValue}
+			}
+		})
+	}
+
+	// Update children
+	if childrenVal := table.RawGetString("_children"); childrenVal.Type() == lua.LTTable {
+		childrenTable := childrenVal.(*lua.LTable)
+		newChildren := []*XMLElement{}
+
+		// Iterate over array indices
+		for i := 1; ; i++ {
+			childVal := childrenTable.RawGetInt(i)
+			if childVal.Type() == lua.LTNil {
+				break
+			}
+			if childVal.Type() == lua.LTTable {
+				if i-1 < len(elem.Children) {
+					// Update existing child
+					luaTableToXMLElement(L, childVal.(*lua.LTable), elem.Children[i-1])
+					newChildren = append(newChildren, elem.Children[i-1])
+				}
+			}
+		}
+		elem.Children = newChildren
+	}
+}

processor/xml_integration_test.go

@@ -0,0 +1,346 @@
+package processor
+
+import (
+	"strings"
+	"testing"
+
+	"cook/utils"
+)
+
+// TestRealWorldGameXML tests with game-like XML structure
+func TestRealWorldGameXML(t *testing.T) {
+	original := `<?xml version="1.0" encoding="utf-8"?>
+<Items>
+  <Item name="Fiber" identifier="Item_Fiber" category="Resource">
+    <Icon texture="Items/Fiber.png" />
+    <Weight value="0.01" />
+    <MaxStack value="1000" />
+    <Description text="Soft plant fibers useful for crafting." />
+  </Item>
+  <Item name="Wood" identifier="Item_Wood" category="Resource">
+    <Icon texture="Items/Wood.png" />
+    <Weight value="0.05" />
+    <MaxStack value="500" />
+    <Description text="Basic building material." />
+  </Item>
+</Items>`
+
+	// Parse
+	origElem, err := parseXMLWithPositions(original)
+	if err != nil {
+		t.Fatalf("Failed to parse: %v", err)
+	}
+
+	// Modify: Double all MaxStack values and change Wood weight
+	modElem := deepCopyXMLElement(origElem)
+
+	// Fiber MaxStack: 1000 → 2000
+	fiberItem := modElem.Children[0]
+	fiberMaxStack := fiberItem.Children[2]
+	valueAttr := fiberMaxStack.Attributes["value"]
+	valueAttr.Value = "2000"
+	fiberMaxStack.Attributes["value"] = valueAttr
+
+	// Wood MaxStack: 500 → 1000
+	woodItem := modElem.Children[1]
+	woodMaxStack := woodItem.Children[2]
+	valueAttr2 := woodMaxStack.Attributes["value"]
+	valueAttr2.Value = "1000"
+	woodMaxStack.Attributes["value"] = valueAttr2
+
+	// Wood Weight: 0.05 → 0.10
+	woodWeight := woodItem.Children[1]
+	weightAttr := woodWeight.Attributes["value"]
+	weightAttr.Value = "0.10"
+	woodWeight.Attributes["value"] = weightAttr
+
+	// Generate changes
+	changes := findXMLChanges(origElem, modElem, "")
+
+	if len(changes) != 3 {
+		t.Fatalf("Expected 3 changes, got %d", len(changes))
+	}
+
+	// Apply
+	commands := applyXMLChanges(changes)
+	result, _ := utils.ExecuteModifications(commands, original)
+
+	// Verify changes
+	if !strings.Contains(result, `<MaxStack value="2000"`) {
+		t.Errorf("Failed to update Fiber MaxStack")
+	}
+	if !strings.Contains(result, `<MaxStack value="1000"`) {
+		t.Errorf("Failed to update Wood MaxStack")
+	}
+	if !strings.Contains(result, `<Weight value="0.10"`) {
+		t.Errorf("Failed to update Wood Weight")
+	}
+
+	// Verify formatting preserved (check XML declaration and indentation)
+	if !strings.HasPrefix(result, `<?xml version="1.0" encoding="utf-8"?>`) {
+		t.Errorf("XML declaration not preserved")
+	}
+	if !strings.Contains(result, "\n  <Item") {
+		t.Errorf("Indentation not preserved")
+	}
+}
+
+// TestAddRemoveMultipleChildren tests adding and removing multiple elements
+func TestAddRemoveMultipleChildren(t *testing.T) {
+	original := `<inventory>
+  <item name="sword" />
+  <item name="shield" />
+  <item name="potion" />
+  <item name="scroll" />
+</inventory>`
+
+	// Parse
+	origElem, err := parseXMLWithPositions(original)
+	if err != nil {
+		t.Fatalf("Failed to parse: %v", err)
+	}
+
+	// Remove middle two items, add a new one
+	modElem := deepCopyXMLElement(origElem)
+
+	// Remove shield and potion (indices 1 and 2)
+	modElem.Children = []*XMLElement{
+		modElem.Children[0], // sword
+		modElem.Children[3], // scroll
+	}
+
+	// Add a new item
+	newItem := &XMLElement{
+		Tag: "item",
+		Attributes: map[string]XMLAttribute{
+			"name": {Value: "helmet"},
+		},
+		Children: []*XMLElement{},
+	}
+	modElem.Children = append(modElem.Children, newItem)
+
+	// Generate changes
+	changes := findXMLChanges(origElem, modElem, "")
+
+	// The algorithm compares by matching indices:
+	// orig[0]=sword vs mod[0]=sword (no change)
+	// orig[1]=shield vs mod[1]=scroll (treated as replace - shows as attribute changes)
+	// orig[2]=potion vs mod[2]=helmet (treated as replace)
+	// orig[3]=scroll (removed)
+	// This is fine - the actual edits will be correct
+
+	if len(changes) == 0 {
+		t.Fatalf("Expected changes, got none")
+	}
+
+	// Apply
+	commands := applyXMLChanges(changes)
+	result, _ := utils.ExecuteModifications(commands, original)
+
+	// Verify
+	if strings.Contains(result, `name="shield"`) {
+		t.Errorf("Shield not removed")
+	}
+	if strings.Contains(result, `name="potion"`) {
+		t.Errorf("Potion not removed")
+	}
+	if !strings.Contains(result, `name="sword"`) {
+		t.Errorf("Sword incorrectly removed")
+	}
+	if !strings.Contains(result, `name="scroll"`) {
+		t.Errorf("Scroll incorrectly removed")
+	}
+	if !strings.Contains(result, `name="helmet"`) {
+		t.Errorf("Helmet not added")
+	}
+}
+
+// TestModifyAttributesAndText tests changing both attributes and text content
+func TestModifyAttributesAndText(t *testing.T) {
+	original := `<weapon>
+  <item type="sword" damage="10">Iron Sword</item>
+  <item type="axe" damage="15">Battle Axe</item>
+</weapon>`
+
+	// Parse
+	origElem, err := parseXMLWithPositions(original)
+	if err != nil {
+		t.Fatalf("Failed to parse: %v", err)
+	}
+
+	// Modify both items
+	modElem := deepCopyXMLElement(origElem)
+
+	// First item: change damage and text
+	item1 := modElem.Children[0]
+	dmgAttr := item1.Attributes["damage"]
+	dmgAttr.Value = "20"
+	item1.Attributes["damage"] = dmgAttr
+	item1.Text = "Steel Sword"
+
+	// Second item: change damage and type
+	item2 := modElem.Children[1]
+	dmgAttr2 := item2.Attributes["damage"]
+	dmgAttr2.Value = "30"
+	item2.Attributes["damage"] = dmgAttr2
+	typeAttr := item2.Attributes["type"]
+	typeAttr.Value = "greataxe"
+	item2.Attributes["type"] = typeAttr
+
+	// Generate and apply changes
+	changes := findXMLChanges(origElem, modElem, "")
+	commands := applyXMLChanges(changes)
+	result, _ := utils.ExecuteModifications(commands, original)
+
+	// Verify
+	if !strings.Contains(result, `damage="20"`) {
+		t.Errorf("First item damage not updated")
+	}
+	if !strings.Contains(result, "Steel Sword") {
+		t.Errorf("First item text not updated")
+	}
+	if !strings.Contains(result, `damage="30"`) {
+		t.Errorf("Second item damage not updated")
+	}
+	if !strings.Contains(result, `type="greataxe"`) {
+		t.Errorf("Second item type not updated")
+	}
+	if strings.Contains(result, "Iron Sword") {
+		t.Errorf("Old text still present")
+	}
+}
+
+// TestSelfClosingTagPreservation tests that self-closing tags work correctly
+func TestSelfClosingTagPreservation(t *testing.T) {
+	original := `<root>
+  <item name="test" />
+  <empty></empty>
+</root>`
+
+	// Parse
+	origElem, err := parseXMLWithPositions(original)
+	if err != nil {
+		t.Fatalf("Failed to parse: %v", err)
+	}
+
+	// Modify first item's attribute
+	modElem := deepCopyXMLElement(origElem)
+	item := modElem.Children[0]
+	nameAttr := item.Attributes["name"]
+	nameAttr.Value = "modified"
+	item.Attributes["name"] = nameAttr
+
+	// Generate and apply changes
+	changes := findXMLChanges(origElem, modElem, "")
+	commands := applyXMLChanges(changes)
+	result, _ := utils.ExecuteModifications(commands, original)
+
+	// Verify the change was made
+	if !strings.Contains(result, `name="modified"`) {
+		t.Errorf("Attribute not updated: %s", result)
+	}
+}
+
+// TestNumericAttributeModification tests numeric attribute changes
+func TestNumericAttributeModification(t *testing.T) {
+	original := `<stats health="100" mana="50" stamina="75.5" />`
+
+	// Parse
+	origElem, err := parseXMLWithPositions(original)
+	if err != nil {
+		t.Fatalf("Failed to parse: %v", err)
+	}
+
+	// Double all numeric values
+	modElem := deepCopyXMLElement(origElem)
+
+	// Helper to modify numeric attributes
+	modifyNumericAttr := func(attrName string, multiplier float64) {
+		if attr, exists := modElem.Attributes[attrName]; exists {
+			if val, ok := parseNumeric(attr.Value); ok {
+				attr.Value = formatNumeric(val * multiplier)
+				modElem.Attributes[attrName] = attr
+			}
+		}
+	}
+
+	modifyNumericAttr("health", 2.0)
+	modifyNumericAttr("mana", 2.0)
+	modifyNumericAttr("stamina", 2.0)
+
+	// Generate and apply changes
+	changes := findXMLChanges(origElem, modElem, "")
+
+	if len(changes) != 3 {
+		t.Fatalf("Expected 3 changes, got %d", len(changes))
+	}
+
+	commands := applyXMLChanges(changes)
+	result, _ := utils.ExecuteModifications(commands, original)
+
+	// Verify numeric changes
+	if !strings.Contains(result, `health="200"`) {
+		t.Errorf("Health not doubled: %s", result)
+	}
+	if !strings.Contains(result, `mana="100"`) {
+		t.Errorf("Mana not doubled: %s", result)
+	}
+	if !strings.Contains(result, `stamina="151"`) {
+		t.Errorf("Stamina not doubled: %s", result)
+	}
+}
+
+// TestMinimalGitDiff verifies that only changed parts are modified
+func TestMinimalGitDiff(t *testing.T) {
+	original := `<config>
+  <setting name="volume" value="50" />
+  <setting name="brightness" value="75" />
+  <setting name="contrast" value="100" />
+</config>`
+
+	// Parse
+	origElem, err := parseXMLWithPositions(original)
+	if err != nil {
+		t.Fatalf("Failed to parse: %v", err)
+	}
+
+	// Change only brightness
+	modElem := deepCopyXMLElement(origElem)
+	brightnessItem := modElem.Children[1]
+	valueAttr := brightnessItem.Attributes["value"]
+	valueAttr.Value = "90"
+	brightnessItem.Attributes["value"] = valueAttr
+
+	// Generate changes
+	changes := findXMLChanges(origElem, modElem, "")
+
+	// Should be exactly 1 change
+	if len(changes) != 1 {
+		t.Fatalf("Expected exactly 1 change for minimal diff, got %d", len(changes))
+	}
+
+	if changes[0].OldValue != "75" || changes[0].NewValue != "90" {
+		t.Errorf("Wrong change detected: %v", changes[0])
+	}
+
+	// Apply
+	commands := applyXMLChanges(changes)
+	result, _ := utils.ExecuteModifications(commands, original)
+
+	// Calculate diff size (rough approximation)
+	diffChars := len(changes[0].OldValue) + len(changes[0].NewValue)
+	if diffChars > 10 {
+		t.Errorf("Diff too large: %d characters changed (expected < 10)", diffChars)
+	}
+
+	// Verify only brightness changed
+	if !strings.Contains(result, `value="50"`) {
+		t.Errorf("Volume incorrectly modified")
+	}
+	if !strings.Contains(result, `value="90"`) {
+		t.Errorf("Brightness not modified")
+	}
+	if !strings.Contains(result, `value="100"`) {
+		t.Errorf("Contrast incorrectly modified")
+	}
+}

processor/xml_real_test.go

@@ -0,0 +1,165 @@
+package processor
+
+import (
+	"os"
+	"strings"
+	"testing"
+
+	"cook/utils"
+)
+
+func TestRealAfflictionsXML(t *testing.T) {
+	// Read the real Afflictions.xml file
+	content, err := os.ReadFile("../testfiles/Afflictions.xml")
+	if err != nil {
+		t.Fatalf("Failed to read Afflictions.xml: %v", err)
+	}
+
+	original := string(content)
+
+	// Test 1: Double all maxstrength values using helper functions
+	command := utils.ModifyCommand{
+		Name: "double_maxstrength",
+		Lua: `
+-- Double all maxstrength attributes in Affliction elements
+local afflictions = findElements(root, "Affliction")
+for _, affliction in ipairs(afflictions) do
+  modifyNumAttr(affliction, "maxstrength", function(val) return val * 2 end)
+end
+modified = true
+`,
+	}
+
+	commands, err := ProcessXML(original, command, "Afflictions.xml")
+	if err != nil {
+		t.Fatalf("ProcessXML failed: %v", err)
+	}
+
+	if len(commands) == 0 {
+		t.Fatal("Expected modifications but got none")
+	}
+
+	t.Logf("Generated %d surgical modifications", len(commands))
+
+	// Apply modifications
+	result, count := utils.ExecuteModifications(commands, original)
+
+	t.Logf("Applied %d modifications", count)
+
+	// Verify specific changes
+	if !strings.Contains(result, `maxstrength="20"`) {
+		t.Errorf("Expected to find maxstrength=\"20\" (doubled from 10)")
+	}
+	if !strings.Contains(result, `maxstrength="480"`) {
+		t.Errorf("Expected to find maxstrength=\"480\" (doubled from 240)")
+	}
+	if !strings.Contains(result, `maxstrength="12"`) {
+		t.Errorf("Expected to find maxstrength=\"12\" (doubled from 6)")
+	}
+
+	// Verify formatting preserved (XML declaration should be there)
+	if !strings.Contains(result, `<?xml`) {
+		t.Errorf("XML declaration not preserved")
+	}
+
+	// Count lines to ensure structure preserved
+	origLines := len(strings.Split(original, "\n"))
+	resultLines := len(strings.Split(result, "\n"))
+	if origLines != resultLines {
+		t.Errorf("Line count changed: original %d, result %d", origLines, resultLines)
+	}
+}
+
+func TestRealAfflictionsAttributes(t *testing.T) {
+	// Read the real file
+	content, err := os.ReadFile("../testfiles/Afflictions.xml")
+	if err != nil {
+		t.Fatalf("Failed to read Afflictions.xml: %v", err)
+	}
+
+	original := string(content)
+
+	// Test 2: Modify resistance values using helper functions
+	command := utils.ModifyCommand{
+		Name: "increase_resistance",
+		Lua: `
+-- Increase all minresistance and maxresistance by 50%
+local effects = findElements(root, "Effect")
+for _, effect in ipairs(effects) do
+  modifyNumAttr(effect, "minresistance", function(val) return val * 1.5 end)
+  modifyNumAttr(effect, "maxresistance", function(val) return val * 1.5 end)
+end
+modified = true
+`,
+	}
+
+	commands, err := ProcessXML(original, command, "Afflictions.xml")
+	if err != nil {
+		t.Fatalf("ProcessXML failed: %v", err)
+	}
+
+	if len(commands) == 0 {
+		t.Fatal("Expected modifications but got none")
+	}
+
+	t.Logf("Generated %d surgical modifications", len(commands))
+
+	// Apply modifications
+	_, count := utils.ExecuteModifications(commands, original)
+
+	t.Logf("Applied %d modifications", count)
+
+	// Verify we made resistance modifications
+	if count < 10 {
+		t.Errorf("Expected at least 10 resistance modifications, got %d", count)
+	}
+}
+
+func TestRealAfflictionsNestedModifications(t *testing.T) {
+	// Read the real file
+	content, err := os.ReadFile("../testfiles/Afflictions.xml")
+	if err != nil {
+		t.Fatalf("Failed to read Afflictions.xml: %v", err)
+	}
+
+	original := string(content)
+
+	// Test 3: Modify nested Effect attributes using helper functions
+	command := utils.ModifyCommand{
+		Name: "modify_effects",
+		Lua: `
+-- Double all amount values in ReduceAffliction elements
+local reduces = findElements(root, "ReduceAffliction")
+for _, reduce in ipairs(reduces) do
+  modifyNumAttr(reduce, "amount", function(val) return val * 2 end)
+end
+modified = true
+`,
+	}
+
+	commands, err := ProcessXML(original, command, "Afflictions.xml")
+	if err != nil {
+		t.Fatalf("ProcessXML failed: %v", err)
+	}
+
+	if len(commands) == 0 {
+		t.Fatal("Expected modifications but got none")
+	}
+
+	t.Logf("Generated %d surgical modifications for nested elements", len(commands))
+
+	// Apply modifications
+	result, count := utils.ExecuteModifications(commands, original)
+
+	t.Logf("Applied %d modifications", count)
+
+	// Verify nested changes (0.001 * 2 = 0.002)
+	if !strings.Contains(result, `amount="0.002"`) {
+		t.Errorf("Expected to find amount=\"0.002\" (0.001 * 2)")
+	}
+
+	// Verify we modified the nested elements
+	if count < 8 {
+		t.Errorf("Expected at least 8 amount modifications, got %d", count)
+	}
+}

processor/xml_test.go

@@ -0,0 +1,621 @@
+package processor
+
+import (
+	"strings"
+	"testing"
+
+	"cook/utils"
+)
+
+func TestParseXMLWithPositions(t *testing.T) {
+	xml := `<root><item name="test">Hello</item></root>`
+
+	elem, err := parseXMLWithPositions(xml)
+	if err != nil {
+		t.Fatalf("Failed to parse XML: %v", err)
+	}
+
+	if elem.Tag != "root" {
+		t.Errorf("Expected root tag 'root', got '%s'", elem.Tag)
+	}
+
+	if len(elem.Children) != 1 {
+		t.Fatalf("Expected 1 child, got %d", len(elem.Children))
+	}
+
+	child := elem.Children[0]
+	if child.Tag != "item" {
+		t.Errorf("Expected child tag 'item', got '%s'", child.Tag)
+	}
+
+	if child.Attributes["name"].Value != "test" {
+		t.Errorf("Expected attribute 'name' to be 'test', got '%s'", child.Attributes["name"].Value)
+	}
+
+	if child.Text != "Hello" {
+		t.Errorf("Expected text 'Hello', got '%s'", child.Text)
+	}
+}
+
+func TestSurgicalTextChange(t *testing.T) {
+	original := `<root>
+  <item name="sword" weight="10">A sword</item>
+</root>`
+
+	expected := `<root>
+  <item name="sword" weight="10">A modified sword</item>
+</root>`
+
+	// Parse original
+	origElem, err := parseXMLWithPositions(original)
+	if err != nil {
+		t.Fatalf("Failed to parse original XML: %v", err)
+	}
+
+	// Create modified version
+	modElem := deepCopyXMLElement(origElem)
+	modElem.Children[0].Text = "A modified sword"
+
+	// Find changes
+	changes := findXMLChanges(origElem, modElem, "")
+
+	if len(changes) != 1 {
+		t.Fatalf("Expected 1 change, got %d", len(changes))
+	}
+
+	if changes[0].Type != "text" {
+		t.Errorf("Expected change type 'text', got '%s'", changes[0].Type)
+	}
+
+	// Apply changes
+	commands := applyXMLChanges(changes)
+	result, _ := utils.ExecuteModifications(commands, original)
+
+	if result != expected {
+		t.Errorf("Text change failed.\nExpected:\n%s\n\nGot:\n%s", expected, result)
+	}
+}
+
+func TestSurgicalAttributeChange(t *testing.T) {
+	original := `<root>
+  <item name="sword" weight="10" />
+</root>`
+
+	expected := `<root>
+  <item name="sword" weight="20" />
+</root>`
+
+	// Parse original
+	origElem, err := parseXMLWithPositions(original)
+	if err != nil {
+		t.Fatalf("Failed to parse original XML: %v", err)
+	}
+
+	// Create modified version
+	modElem := deepCopyXMLElement(origElem)
+	attr := modElem.Children[0].Attributes["weight"]
+	attr.Value = "20"
+	modElem.Children[0].Attributes["weight"] = attr
+
+	// Find changes
+	changes := findXMLChanges(origElem, modElem, "")
+
+	if len(changes) != 1 {
+		t.Fatalf("Expected 1 change, got %d", len(changes))
+	}
+
+	if changes[0].Type != "attribute" {
+		t.Errorf("Expected change type 'attribute', got '%s'", changes[0].Type)
+	}
+
+	// Apply changes
+	commands := applyXMLChanges(changes)
+	result, _ := utils.ExecuteModifications(commands, original)
+
+	if result != expected {
+		t.Errorf("Attribute change failed.\nExpected:\n%s\n\nGot:\n%s", expected, result)
+	}
+}
+
+func TestSurgicalMultipleAttributeChanges(t *testing.T) {
+	original := `<item name="sword" weight="10" damage="5" />`
+
+	expected := `<item name="greatsword" weight="20" damage="15" />`
+
+	// Parse original
+	origElem, err := parseXMLWithPositions(original)
+	if err != nil {
+		t.Fatalf("Failed to parse original XML: %v", err)
+	}
+
+	// Create modified version
+	modElem := deepCopyXMLElement(origElem)
+
+	nameAttr := modElem.Attributes["name"]
+	nameAttr.Value = "greatsword"
+	modElem.Attributes["name"] = nameAttr
+
+	weightAttr := modElem.Attributes["weight"]
+	weightAttr.Value = "20"
+	modElem.Attributes["weight"] = weightAttr
+
+	damageAttr := modElem.Attributes["damage"]
+	damageAttr.Value = "15"
+	modElem.Attributes["damage"] = damageAttr
+
+	// Find changes
+	changes := findXMLChanges(origElem, modElem, "")
+
+	if len(changes) != 3 {
+		t.Fatalf("Expected 3 changes, got %d", len(changes))
+	}
+
+	// Apply changes
+	commands := applyXMLChanges(changes)
+	result, _ := utils.ExecuteModifications(commands, original)
+
+	if result != expected {
+		t.Errorf("Multiple attribute changes failed.\nExpected:\n%s\n\nGot:\n%s", expected, result)
+	}
+}
+
+func TestSurgicalAddAttribute(t *testing.T) {
+	original := `<item name="sword" />`
+
+	// Parse original
+	origElem, err := parseXMLWithPositions(original)
+	if err != nil {
+		t.Fatalf("Failed to parse original XML: %v", err)
+	}
+
+	// Create modified version with new attribute
+	modElem := deepCopyXMLElement(origElem)
+	modElem.Attributes["weight"] = XMLAttribute{
+		Value: "10",
+	}
+
+	// Find changes
+	changes := findXMLChanges(origElem, modElem, "")
+
+	if len(changes) != 1 {
+		t.Fatalf("Expected 1 change, got %d", len(changes))
+	}
+
+	if changes[0].Type != "add_attribute" {
+		t.Errorf("Expected change type 'add_attribute', got '%s'", changes[0].Type)
+	}
+
+	// Apply changes
+	commands := applyXMLChanges(changes)
+	result, _ := utils.ExecuteModifications(commands, original)
+
+	// Should contain the new attribute
+	if !strings.Contains(result, `weight="10"`) {
+		t.Errorf("Add attribute failed. Result doesn't contain weight=\"10\":\n%s", result)
+	}
+}
+
+func TestSurgicalRemoveAttribute(t *testing.T) {
+	original := `<item name="sword" weight="10" damage="5" />`
+
+	// Parse original
+	origElem, err := parseXMLWithPositions(original)
+	if err != nil {
+		t.Fatalf("Failed to parse original XML: %v", err)
+	}
+
+	// Create modified version without weight attribute
+	modElem := deepCopyXMLElement(origElem)
+	delete(modElem.Attributes, "weight")
+
+	// Find changes
+	changes := findXMLChanges(origElem, modElem, "")
+
+	if len(changes) != 1 {
+		t.Fatalf("Expected 1 change, got %d", len(changes))
+	}
+
+	if changes[0].Type != "remove_attribute" {
+		t.Errorf("Expected change type 'remove_attribute', got '%s'", changes[0].Type)
+	}
+
+	// Apply changes
+	commands := applyXMLChanges(changes)
+	result, _ := utils.ExecuteModifications(commands, original)
+
+	// Should not contain weight attribute
+	if strings.Contains(result, "weight=") {
+		t.Errorf("Remove attribute failed. Result still contains 'weight=':\n%s", result)
+	}
+
+	// Should still contain other attributes
+	if !strings.Contains(result, `name="sword"`) {
+		t.Errorf("Remove attribute incorrectly removed other attributes:\n%s", result)
+	}
+}
+
+func TestSurgicalAddElement(t *testing.T) {
+	original := `<root>
+  <item name="sword" />
+</root>`
+
+	// Parse original
+	origElem, err := parseXMLWithPositions(original)
+	if err != nil {
+		t.Fatalf("Failed to parse original XML: %v", err)
+	}
+
+	// Create modified version with new child
+	modElem := deepCopyXMLElement(origElem)
+	newChild := &XMLElement{
+		Tag: "item",
+		Attributes: map[string]XMLAttribute{
+			"name": {Value: "shield"},
+		},
+		Children: []*XMLElement{},
+	}
+	modElem.Children = append(modElem.Children, newChild)
+
+	// Find changes
+	changes := findXMLChanges(origElem, modElem, "")
+
+	if len(changes) != 1 {
+		t.Fatalf("Expected 1 change, got %d", len(changes))
+	}
+
+	if changes[0].Type != "add_element" {
+		t.Errorf("Expected change type 'add_element', got '%s'", changes[0].Type)
+	}
+
+	// Apply changes
+	commands := applyXMLChanges(changes)
+	result, _ := utils.ExecuteModifications(commands, original)
+
+	// Should contain the new element
+	if !strings.Contains(result, `<item name="shield"`) {
+		t.Errorf("Add element failed. Result doesn't contain new item:\n%s", result)
+	}
+}
+
+func TestSurgicalRemoveElement(t *testing.T) {
+	original := `<root>
+  <item name="sword" />
+  <item name="shield" />
+</root>`
+
+	expected := `<root>
+  <item name="sword" />
+  
+</root>`
+
+	// Parse original
+	origElem, err := parseXMLWithPositions(original)
+	if err != nil {
+		t.Fatalf("Failed to parse original XML: %v", err)
+	}
+
+	// Create modified version without second child
+	modElem := deepCopyXMLElement(origElem)
+	modElem.Children = modElem.Children[:1]
+
+	// Find changes
+	changes := findXMLChanges(origElem, modElem, "")
+
+	if len(changes) != 1 {
+		t.Fatalf("Expected 1 change, got %d", len(changes))
+	}
+
+	if changes[0].Type != "remove_element" {
+		t.Errorf("Expected change type 'remove_element', got '%s'", changes[0].Type)
+	}
+
+	// Apply changes
+	commands := applyXMLChanges(changes)
+	result, _ := utils.ExecuteModifications(commands, original)
+
+	// Should not contain shield
+	if strings.Contains(result, "shield") {
+		t.Errorf("Remove element failed. Result still contains 'shield':\n%s", result)
+	}
+
+	// Should still contain sword
+	if !strings.Contains(result, "sword") {
+		t.Errorf("Remove element incorrectly removed other elements:\n%s", result)
+	}
+
+	// Normalize whitespace for comparison
+	resultNorm := strings.TrimSpace(result)
+	expectedNorm := strings.TrimSpace(expected)
+
+	if resultNorm != expectedNorm {
+		t.Errorf("Remove element result mismatch.\nExpected:\n%s\n\nGot:\n%s", expectedNorm, resultNorm)
+	}
+}
+
+func TestComplexNestedChanges(t *testing.T) {
+	original := `<root>
+  <inventory>
+    <item name="sword" weight="10">
+      <stats damage="5" speed="3" />
+    </item>
+    <item name="shield" weight="8">
+      <stats defense="7" />
+    </item>
+  </inventory>
+</root>`
+
+	// Parse original
+	origElem, err := parseXMLWithPositions(original)
+	if err != nil {
+		t.Fatalf("Failed to parse original XML: %v", err)
+	}
+
+	// Create modified version with multiple changes
+	modElem := deepCopyXMLElement(origElem)
+
+	// Change first item's weight
+	inventory := modElem.Children[0]
+	item1 := inventory.Children[0]
+	weightAttr := item1.Attributes["weight"]
+	weightAttr.Value = "20"
+	item1.Attributes["weight"] = weightAttr
+
+	// Change nested stats damage
+	stats := item1.Children[0]
+	damageAttr := stats.Attributes["damage"]
+	damageAttr.Value = "10"
+	stats.Attributes["damage"] = damageAttr
+
+	// Change second item's name
+	item2 := inventory.Children[1]
+	nameAttr := item2.Attributes["name"]
+	nameAttr.Value = "buckler"
+	item2.Attributes["name"] = nameAttr
+
+	// Find changes
+	changes := findXMLChanges(origElem, modElem, "")
+
+	// Should have 3 changes: weight, damage, name
+	if len(changes) != 3 {
+		t.Fatalf("Expected 3 changes, got %d: %+v", len(changes), changes)
+	}
+
+	// Apply changes
+	commands := applyXMLChanges(changes)
+	result, _ := utils.ExecuteModifications(commands, original)
+
+	// Verify all changes were applied
+	if !strings.Contains(result, `weight="20"`) {
+		t.Errorf("Failed to update weight to 20:\n%s", result)
+	}
+	if !strings.Contains(result, `damage="10"`) {
+		t.Errorf("Failed to update damage to 10:\n%s", result)
+	}
+	if !strings.Contains(result, `name="buckler"`) {
+		t.Errorf("Failed to update name to buckler:\n%s", result)
+	}
+
+	// Verify unchanged elements remain
+	if !strings.Contains(result, `speed="3"`) {
+		t.Errorf("Incorrectly modified speed attribute:\n%s", result)
+	}
+	if !strings.Contains(result, `defense="7"`) {
+		t.Errorf("Incorrectly modified defense attribute:\n%s", result)
+	}
+}
+
+func TestFormattingPreservation(t *testing.T) {
+	original := `<root>
+  <item name="sword" weight="10">
+    <description>A sharp blade</description>
+    <stats damage="5" speed="3" />
+  </item>
+</root>`
+
+	expected := `<root>
+  <item name="sword" weight="20">
+    <description>A sharp blade</description>
+    <stats damage="5" speed="3" />
+  </item>
+</root>`
+
+	// Parse original
+	origElem, err := parseXMLWithPositions(original)
+	if err != nil {
+		t.Fatalf("Failed to parse original XML: %v", err)
+	}
+
+	// Modify only weight
+	modElem := deepCopyXMLElement(origElem)
+	item := modElem.Children[0]
+	weightAttr := item.Attributes["weight"]
+	weightAttr.Value = "20"
+	item.Attributes["weight"] = weightAttr
+
+	// Find changes
+	changes := findXMLChanges(origElem, modElem, "")
+
+	// Apply changes
+	commands := applyXMLChanges(changes)
+	result, _ := utils.ExecuteModifications(commands, original)
+
+	if result != expected {
+		t.Errorf("Formatting preservation failed.\nExpected:\n%s\n\nGot:\n%s", expected, result)
+	}
+}
+
+func TestNumericHelpers(t *testing.T) {
+	tests := []struct {
+		input    string
+		expected float64
+		isNum    bool
+	}{
+		{"42", 42.0, true},
+		{"3.14", 3.14, true},
+		{"0", 0.0, true},
+		{"-5", -5.0, true},
+		{"abc", 0.0, false},
+		{"", 0.0, false},
+	}
+
+	for _, tt := range tests {
+		val, ok := parseNumeric(tt.input)
+		if ok != tt.isNum {
+			t.Errorf("parseNumeric(%q) isNum = %v, expected %v", tt.input, ok, tt.isNum)
+		}
+		if ok && val != tt.expected {
+			t.Errorf("parseNumeric(%q) = %v, expected %v", tt.input, val, tt.expected)
+		}
+	}
+
+	// Test formatting
+	formatTests := []struct {
+		input    float64
+		expected string
+	}{
+		{42.0, "42"},
+		{3.14, "3.14"},
+		{0.0, "0"},
+		{-5.0, "-5"},
+		{100.5, "100.5"},
+	}
+
+	for _, tt := range formatTests {
+		result := formatNumeric(tt.input)
+		if result != tt.expected {
+			t.Errorf("formatNumeric(%v) = %q, expected %q", tt.input, result, tt.expected)
+		}
+	}
+}
+
+func TestDeepCopyXMLElement(t *testing.T) {
+	original := &XMLElement{
+		Tag:  "item",
+		Text: "content",
+		Attributes: map[string]XMLAttribute{
+			"name": {Value: "sword"},
+		},
+		Children: []*XMLElement{
+			{Tag: "child", Text: "text"},
+		},
+	}
+
+	copied := deepCopyXMLElement(original)
+
+	// Verify copy is equal
+	if copied.Tag != original.Tag {
+		t.Errorf("Tag not copied correctly")
+	}
+	if copied.Text != original.Text {
+		t.Errorf("Text not copied correctly")
+	}
+
+	// Modify copy
+	copied.Tag = "modified"
+	copied.Attributes["name"] = XMLAttribute{Value: "shield"}
+	copied.Children[0].Text = "modified text"
+
+	// Verify original unchanged
+	if original.Tag != "item" {
+		t.Errorf("Original was modified")
+	}
+	if original.Attributes["name"].Value != "sword" {
+		t.Errorf("Original attributes were modified")
+	}
+	if original.Children[0].Text != "text" {
+		t.Errorf("Original children were modified")
+	}
+}
+
+func TestSerializeXMLElement(t *testing.T) {
+	elem := &XMLElement{
+		Tag: "item",
+		Attributes: map[string]XMLAttribute{
+			"name":   {Value: "sword"},
+			"weight": {Value: "10"},
+		},
+		Children: []*XMLElement{
+			{
+				Tag: "stats",
+				Attributes: map[string]XMLAttribute{
+					"damage": {Value: "5"},
+				},
+				Children: []*XMLElement{},
+			},
+		},
+	}
+
+	result := serializeXMLElement(elem, "")
+
+	// Check it contains expected parts
+	if !strings.Contains(result, "<item") {
+		t.Errorf("Missing opening tag")
+	}
+	if !strings.Contains(result, "</item>") {
+		t.Errorf("Missing closing tag")
+	}
+	if !strings.Contains(result, `name="sword"`) {
+		t.Errorf("Missing name attribute")
+	}
+	if !strings.Contains(result, `weight="10"`) {
+		t.Errorf("Missing weight attribute")
+	}
+	if !strings.Contains(result, "<stats") {
+		t.Errorf("Missing child element")
+	}
+}
+
+func TestEmptyElements(t *testing.T) {
+	original := `<root>
+  <item name="sword" />
+  <item name="shield"></item>
+</root>`
+
+	// Parse
+	elem, err := parseXMLWithPositions(original)
+	if err != nil {
+		t.Fatalf("Failed to parse XML: %v", err)
+	}
+
+	if len(elem.Children) != 2 {
+		t.Errorf("Expected 2 children, got %d", len(elem.Children))
+	}
+
+	// Both should be parsed correctly
+	if elem.Children[0].Tag != "item" {
+		t.Errorf("First child tag incorrect")
+	}
+	if elem.Children[1].Tag != "item" {
+		t.Errorf("Second child tag incorrect")
+	}
+}
+
+func TestAttributeOrderPreservation(t *testing.T) {
+	original := `<item name="sword" weight="10" damage="5" speed="3" />`
+
+	// Parse original
+	origElem, err := parseXMLWithPositions(original)
+	if err != nil {
+		t.Fatalf("Failed to parse original XML: %v", err)
+	}
+
+	// Modify just weight
+	modElem := deepCopyXMLElement(origElem)
+	weightAttr := modElem.Attributes["weight"]
+	weightAttr.Value = "20"
+	modElem.Attributes["weight"] = weightAttr
+
+	// Find and apply changes
+	changes := findXMLChanges(origElem, modElem, "")
+	commands := applyXMLChanges(changes)
+	result, _ := utils.ExecuteModifications(commands, original)
+
+	// Verify attribute order is preserved (weight comes before damage and speed)
+	weightIdx := strings.Index(result, "weight=")
+	damageIdx := strings.Index(result, "damage=")
+	speedIdx := strings.Index(result, "speed=")
+
+	if weightIdx > damageIdx || damageIdx > speedIdx {
+		t.Errorf("Attribute order not preserved:\n%s", result)
+	}
+}

regression/regression_test.go

@@ -1,8 +1,8 @@
 package regression
 
 import (
-	"modify/processor"
-	"modify/utils"
+	"cook/processor"
+	"cook/utils"
 	"os"
 	"path/filepath"
 	"testing"
@@ -15,7 +15,7 @@ func ApiAdaptor(content string, regex string, lua string) (string, int, int, err
 		LogLevel: "TRACE",
 	}
 
-	commands, err := processor.ProcessRegex(content, command)
+	commands, err := processor.ProcessRegex(content, command, "test")
 	if err != nil {
 		return "", 0, 0, err
 	}

test_surgical.yml

@@ -0,0 +1,11 @@
+- name: SurgicalWeightTest
+  json: true
+  lua: |
+    -- This demonstrates surgical JSON editing
+    -- Only the Weight field of Item_Fiber will be modified
+    data.Rows[1].Weight = 999
+    modified = true
+  files:
+    - 'D_Itemable.json'
+  reset: false
+  loglevel: INFO 

testfiles/Afflictions.xml

@@ -0,0 +1,74 @@
+<?xml version="1.0" encoding="utf-8"?>
+<Afflictions>
+  <Affliction name="" identifier="Cozy_Fire" type="strengthbuff" limbspecific="false" isbuff="true" maxstrength="10" hideiconafterdelay="true">
+    <Effect minstrength="0" maxstrength="10" strengthchange="-1.0">
+      <ReduceAffliction type="damage" amount="0.001" />
+      <ReduceAffliction type="bleeding" amount="0.001" />
+      <ReduceAffliction type="burn" amount="0.001" />
+      <ReduceAffliction type="bloodloss" amount="0.001" />
+    </Effect>
+    <icon texture="%ModDir%/Placable/Cozy_Fire.png" sourcerect="0,0,64,64" origin="0,0" />
+  </Affliction>
+  <Affliction name="" identifier="The_Bast_Defense" type="strengthbuff" limbspecific="false" isbuff="true" maxstrength="10" hideiconafterdelay="true">
+    <Effect minstrength="0" maxstrength="10" strengthchange="-1.0" resistancefor="damage" minresistance="0.05" maxresistance="0.05"></Effect>
+    <icon texture="%ModDir%/Placable/The_Bast_Defense.png" sourcerect="0,0,64,64" origin="0,0" />
+  </Affliction>
+  <Affliction name="" identifier="Clairvoyance" type="strengthbuff" limbspecific="false" isbuff="true" maxstrength="240" hideiconafterdelay="true">
+    <Effect minstrength="0" maxstrength="240" strengthchange="-1.0" resistancefor="stun" minresistance="0.15" maxresistance="0.15"></Effect>
+    <icon texture="%ModDir%/Placable/Clairvoyance.png" sourcerect="0,0,64,64" origin="0,0" />
+  </Affliction>
+  <Affliction name="" identifier="Heart_Lamp" type="strengthbuff" limbspecific="false" isbuff="true" maxstrength="10" hideiconafterdelay="true">
+    <Effect minstrength="0" maxstrength="10" strengthchange="-1.0">
+      <ReduceAffliction type="damage" amount="0.001" />
+      <ReduceAffliction type="bleeding" amount="0.001" />
+      <ReduceAffliction type="burn" amount="0.001" />
+      <ReduceAffliction type="bloodloss" amount="0.001" />
+    </Effect>
+    <icon texture="%ModDir%/Placable/Heart_Lamp.png" sourcerect="0,0,64,64" origin="0,0" />
+  </Affliction>
+  <Affliction name="" identifier="Star_in_a_Bottle_buff" type="strengthbuff" limbspecific="false" isbuff="true" maxstrength="10" hideiconafterdelay="true">
+    <Effect minstrength="0" maxstrength="10" strengthchange="-1.0" resistancefor="stun" minresistance="0.1" maxresistance="0.1"></Effect>
+    <icon texture="%ModDir%/Placable/Star_in_a_Bottle_buff.png" sourcerect="0,0,64,64" origin="0,0" />
+  </Affliction>
+  <Affliction name="" identifier="HappyF" type="strengthbuff" limbspecific="false" isbuff="true" maxstrength="10" hideiconafterdelay="true">
+    <Effect minstrength="0" maxstrength="10" strengthchange="-1.0" resistancefor="stun" minresistance="0.05" maxresistance="0.05" minspeedmultiplier="1.1" maxspeedmultiplier="1.1"></Effect>
+    <icon texture="%ModDir%/Placable/Happy.png" sourcerect="0,0,64,64" origin="0,0" />
+  </Affliction>
+  <Affliction name="" identifier="SharpenedF" type="strengthbuff" limbspecific="false" isbuff="true" maxstrength="240" hideiconafterdelay="true">
+    <Effect minstrength="0" maxstrength="240" strengthchange="-1.0">
+      <StatValue stattype="MeleeAttackMultiplier" value="0.25" />
+    </Effect>
+    <icon texture="%ModDir%/Placable/Sharpened.png" sourcerect="0,0,64,64" origin="0,0" />
+  </Affliction>
+  <Affliction name="" identifier="Sugar_RushF" type="strengthbuff" limbspecific="false" isbuff="true" maxstrength="240" hideiconafterdelay="true">
+    <Effect minstrength="0" maxstrength="240" strengthchange="-1.0" minspeedmultiplier="1.2" maxspeedmultiplier="1.2">
+      <StatValue stattype="MeleeAttackSpeed" value="0.05" />
+      <StatValue stattype="RangedAttackSpeed" value="0.05" />
+    </Effect>
+    <icon texture="%ModDir%/Placable/Sugar_Rush.png" sourcerect="0,0,64,64" origin="0,0" />
+  </Affliction>
+  <Affliction name="" identifier="Crimson_Effigy_buff" type="strengthbuff" limbspecific="false" isbuff="true" maxstrength="240" hideiconafterdelay="true">
+    <Effect minstrength="0" maxstrength="240" strengthchange="-1.0" resistancefor="damage" minresistance="-0.1" maxresistance="-0.1">
+      <StatValue stattype="MeleeAttackSpeed" value="0.15" />
+      <StatValue stattype="RangedAttackSpeed" value="0.15" />
+    </Effect>
+    <icon texture="%ModDir%/Placable/Crimson_Effigy_buff.png" sourcerect="0,0,64,64" origin="0,0" />
+  </Affliction>
+  <Affliction name="" identifier="Corruption_Effigy_buff" type="strengthbuff" limbspecific="false" isbuff="true" maxstrength="240" hideiconafterdelay="true">
+    <Effect minstrength="0" maxstrength="240" strengthchange="-1.0" minvitalitydecrease="0.2" multiplybymaxvitality="true" maxvitalitydecrease="0.2" resistancefor="damage" minresistance="0.1" maxresistance="0.1">
+      <StatValue stattype="AttackMultiplier" value="0.2" />
+    </Effect>
+    <icon texture="%ModDir%/Placable/Corruption_Effigy_buff.png" sourcerect="0,0,64,64" origin="0,0" />
+  </Affliction>
+  <Affliction name="" identifier="Effigy_of_Decay_buff" type="strengthbuff" limbspecific="false" isbuff="true" maxstrength="240" hideiconafterdelay="true">
+    <Effect minstrength="0" maxstrength="240" strengthchange="-1.0" resistancefor="oxygenlow" minresistance="1" maxresistance="1">
+      <StatusEffect target="Character" SpeedMultiplier="1.1" OxygenAvailable="1000.0" setvalue="true" />
+      <AbilityFlag flagtype="ImmuneToPressure" />
+    </Effect>
+    <icon texture="%ModDir%/Placable/Effigy_of_Decay_buff.png" sourcerect="0,0,64,64" origin="0,0" />
+  </Affliction>
+  <Affliction name="" identifier="Chlorophyte_Extractinator" type="strengthbuff" limbspecific="false" isbuff="true" maxstrength="6" hideiconafterdelay="true">
+    <Effect minstrength="0" maxstrength="6" strengthchange="-1.0"></Effect>
+    <icon texture="%ModDir%/Extractinator/Chlorophyte_Extractinator.png" sourcerect="0,0,144,152" origin="0,0" />
+  </Affliction>
+</Afflictions>

testfiles/format_test_cook.yml

@@ -0,0 +1,8 @@
+- name: "JSONFormattingTest"
+  json: true
+  lua: |
+    data.version = "2.0.0"
+    data.enabled = true
+    data.settings.timeout = 60
+    return true
+  files: ["testfiles/test3.json"] 

testfiles/json_global_test_cook.yml

@@ -0,0 +1,15 @@
+# Test with global JSON flag (no json: true in commands)
+- name: "JSONArrayMultiply"
+  lua: |
+    for i, item in ipairs(data.items) do 
+      data.items[i].value = item.value * 2 
+    end
+    return true
+  files: ["testfiles/test2.json"]
+
+- name: "JSONObjectUpdate"
+  lua: |
+    data.version = "3.0.0"
+    data.enabled = false
+    return true
+  files: ["testfiles/test2.json"] 

testfiles/json_test_cook.yml

@@ -0,0 +1,32 @@
+# Global modifiers
+- modifiers:
+    multiply: 2.0
+    new_version: "2.0.0"
+
+# JSON mode examples
+- name: "JSONArrayMultiply"
+  json: true
+  lua: |
+    for i, item in ipairs(data.items) do 
+      data.items[i].value = item.value * $multiply 
+    end
+    return true
+  files: ["testfiles/test.json"]
+
+- name: "JSONObjectUpdate"
+  json: true
+  lua: |
+    data.version = $new_version
+    data.enabled = true
+    return true
+  files: ["testfiles/test.json"]
+
+- name: "JSONNestedModify"
+  json: true
+  lua: |
+    if data.settings and data.settings.performance then 
+      data.settings.performance.multiplier = data.settings.performance.multiplier * 1.5 
+      data.settings.performance.enabled = true
+    end
+    return true
+  files: ["testfiles/test.json"] 

testfiles/test.json

@@ -0,0 +1,30 @@
+{
+  "name": "test-config",
+  "version": "1.0.0",
+  "enabled": false,
+  "settings": {
+    "timeout": 30,
+    "retries": 3,
+    "performance": {
+      "multiplier": 1.0,
+      "enabled": false
+    }
+  },
+  "items": [
+    {
+      "id": 1,
+      "name": "item1",
+      "value": 10
+    },
+    {
+      "id": 2,
+      "name": "item2",
+      "value": 20
+    },
+    {
+      "id": 3,
+      "name": "item3",
+      "value": 30
+    }
+  ]
+} 

testfiles/test2.json

@@ -0,0 +1,30 @@
+{
+  "enabled": false,
+  "items": [
+    {
+      "id": 1,
+      "name": "item1",
+      "value": 80
+    },
+    {
+      "id": 2,
+      "name": "item2",
+      "value": 160
+    },
+    {
+      "id": 3,
+      "name": "item3",
+      "value": 240
+    }
+  ],
+  "name": "test-config",
+  "settings": {
+    "performance": {
+      "enabled": true,
+      "multiplier": 1.5
+    },
+    "retries": 3,
+    "timeout": 30
+  },
+  "version": "3.0.0"
+}

testfiles/test3.json

@@ -0,0 +1,25 @@
+{
+	"enabled": true,
+	"items": [
+		{
+			"id": 1,
+			"name": "item1",
+			"value": 10
+		},
+		{
+			"id": 2,
+			"name": "item2",
+			"value": 20
+		}
+	],
+	"name": "test-config",
+	"settings": {
+		"performance": {
+			"enabled": false,
+			"multiplier": 1
+		},
+		"retries": 3,
+		"timeout": 60
+	},
+	"version": "2.0.0"
+}

testfiles/test3_backup.json

@@ -0,0 +1,25 @@
+{
+	"enabled": true,
+	"items": [
+		{
+			"id": 1,
+			"name": "item1",
+			"value": 10
+		},
+		{
+			"id": 2,
+			"name": "item2",
+			"value": 20
+		}
+	],
+	"name": "test-config",
+	"settings": {
+		"performance": {
+			"enabled": false,
+			"multiplier": 1
+		},
+		"retries": 3,
+		"timeout": 60
+	},
+	"version": "2.0.0"
+}

testfiles/test4.json

@@ -0,0 +1,25 @@
+{
+	"name": "test-config",
+	"version": "1.0.0",
+	"enabled": false,
+	"settings": {
+		"timeout": 30,
+		"retries": 3,
+		"performance": {
+			"multiplier": 1.0,
+			"enabled": false
+		}
+	},
+	"items": [
+		{
+			"id": 1,
+			"name": "item1",
+			"value": 10
+		},
+		{
+			"id": 2,
+			"name": "item2",
+			"value": 20
+		}
+	]
+} 

toml_test.go

@@ -0,0 +1,502 @@
+package main
+
+import (
+	"os"
+	"path/filepath"
+	"testing"
+
+	"cook/utils"
+
+	"github.com/stretchr/testify/assert"
+)
+
+func TestTOMLLoadBasic(t *testing.T) {
+	// Create a temporary directory for testing
+	tmpDir, err := os.MkdirTemp("", "toml-basic-test")
+	if err != nil {
+		t.Fatalf("Failed to create temp dir: %v", err)
+	}
+	defer os.RemoveAll(tmpDir)
+
+	// Create a simple TOML test file
+	tomlContent := `[[commands]]
+name = "SimpleTest"
+regex = "test = !num"
+lua = "v1 * 2"
+files = ["test.txt"]
+
+[[commands]]
+name = "AnotherTest"
+regex = "value = (!num)"
+lua = "v1 + 10"
+files = ["*.txt"]
+`
+
+	tomlFile := filepath.Join(tmpDir, "test.toml")
+	err = os.WriteFile(tomlFile, []byte(tomlContent), 0644)
+	if err != nil {
+		t.Fatalf("Failed to write TOML test file: %v", err)
+	}
+
+	// Change to temp directory
+	origDir, _ := os.Getwd()
+	defer os.Chdir(origDir)
+	os.Chdir(tmpDir)
+
+	// Test loading TOML commands
+	commands, _, err := utils.LoadCommandsFromTomlFiles("test.toml")
+	assert.NoError(t, err, "Should load TOML commands without error")
+	assert.Len(t, commands, 2, "Should load 2 commands from TOML")
+
+	// Verify first command
+	assert.Equal(t, "SimpleTest", commands[0].Name, "First command name should match")
+	assert.Equal(t, "test = !num", commands[0].Regex, "First command regex should match")
+	assert.Equal(t, "v1 * 2", commands[0].Lua, "First command Lua should match")
+	assert.Equal(t, []string{"test.txt"}, commands[0].Files, "First command files should match")
+
+	// Verify second command
+	assert.Equal(t, "AnotherTest", commands[1].Name, "Second command name should match")
+	assert.Equal(t, "value = (!num)", commands[1].Regex, "Second command regex should match")
+	assert.Equal(t, "v1 + 10", commands[1].Lua, "Second command Lua should match")
+	assert.Equal(t, []string{"*.txt"}, commands[1].Files, "Second command files should match")
+}
+
+func TestTOMLGlobalModifiers(t *testing.T) {
+	// Create a temporary directory for testing
+	tmpDir, err := os.MkdirTemp("", "toml-global-modifiers-test")
+	if err != nil {
+		t.Fatalf("Failed to create temp dir: %v", err)
+	}
+	defer os.RemoveAll(tmpDir)
+
+	// Create TOML content with global variables
+	tomlContent := `[variables]
+multiplier = 3
+prefix = "TEST_"
+enabled = true
+
+[[commands]]
+name = "UseGlobalModifiers"
+regex = "value = !num"
+lua = "v1 * multiplier; s1 = prefix .. s1"
+files = ["test.txt"]
+`
+
+	tomlFile := filepath.Join(tmpDir, "test.toml")
+	err = os.WriteFile(tomlFile, []byte(tomlContent), 0644)
+	if err != nil {
+		t.Fatalf("Failed to write TOML test file: %v", err)
+	}
+
+	// Change to temp directory
+	origDir, _ := os.Getwd()
+	defer os.Chdir(origDir)
+	os.Chdir(tmpDir)
+
+	// Test loading TOML commands
+	commands, variables, err := utils.LoadCommandsFromTomlFiles("test.toml")
+	assert.NoError(t, err, "Should load TOML commands without error")
+	assert.Len(t, commands, 1, "Should load 1 command from TOML")
+	assert.Len(t, variables, 3, "Should load 3 variables")
+
+	// Verify variables
+	assert.Equal(t, int64(3), variables["multiplier"], "Multiplier should be 3")
+	assert.Equal(t, "TEST_", variables["prefix"], "Prefix should be TEST_")
+	assert.Equal(t, true, variables["enabled"], "Enabled should be true")
+
+	// Verify regular command
+	assert.Equal(t, "UseGlobalModifiers", commands[0].Name, "Regular command name should match")
+	assert.Equal(t, "value = !num", commands[0].Regex, "Regular command regex should match")
+}
+
+func TestTOMLMultilineRegex(t *testing.T) {
+	// Create a temporary directory for testing
+	tmpDir, err := os.MkdirTemp("", "toml-multiline-test")
+	if err != nil {
+		t.Fatalf("Failed to create temp dir: %v", err)
+	}
+	defer os.RemoveAll(tmpDir)
+
+	// Create TOML content with multiline regex using literal strings
+	tomlContent := `[variables]
+factor = 2.5
+
+[[commands]]
+name = "MultilineTest"
+regex = '''
+\[config\.settings\]
+
+    depth = !num
+
+    width = !num
+
+    height = !num'''
+lua = "v1 * factor"
+files = ["test.conf"]
+isolate = true
+`
+
+	tomlFile := filepath.Join(tmpDir, "test.toml")
+	err = os.WriteFile(tomlFile, []byte(tomlContent), 0644)
+	if err != nil {
+		t.Fatalf("Failed to write TOML test file: %v", err)
+	}
+
+	// Create test file that matches the multiline pattern
+	testContent := `[config.settings]
+
+    depth = 10
+
+    width = 20
+
+    height = 30
+`
+
+	testFile := filepath.Join(tmpDir, "test.conf")
+	err = os.WriteFile(testFile, []byte(testContent), 0644)
+	if err != nil {
+		t.Fatalf("Failed to write test file: %v", err)
+	}
+
+	// Change to temp directory
+	origDir, _ := os.Getwd()
+	defer os.Chdir(origDir)
+	os.Chdir(tmpDir)
+
+	// Test loading TOML commands
+	commands, variables, err := utils.LoadCommandsFromTomlFiles("test.toml")
+	assert.NoError(t, err, "Should load TOML commands without error")
+	assert.Len(t, commands, 1, "Should load 1 command from TOML")
+	assert.Len(t, variables, 1, "Should load 1 variable")
+
+	// Verify the multiline regex command
+	multilineCmd := commands[0]
+	assert.Equal(t, "MultilineTest", multilineCmd.Name, "Command name should match")
+	assert.Contains(t, multilineCmd.Regex, "\\[config\\.settings\\]", "Regex should contain escaped brackets")
+	assert.Contains(t, multilineCmd.Regex, "depth = !num", "Regex should contain depth pattern")
+	assert.Contains(t, multilineCmd.Regex, "width = !num", "Regex should contain width pattern")
+	assert.Contains(t, multilineCmd.Regex, "height = !num", "Regex should contain height pattern")
+	assert.Contains(t, multilineCmd.Regex, "\n", "Regex should contain newlines")
+	assert.True(t, multilineCmd.Isolate, "Isolate should be true")
+
+	// Verify the regex preserves proper structure
+	expectedLines := []string{
+		"\\[config\\.settings\\]",
+		"depth = !num",
+		"width = !num",
+		"height = !num",
+	}
+
+	for _, line := range expectedLines {
+		assert.Contains(t, multilineCmd.Regex, line, "Regex should contain: "+line)
+	}
+}
+
+func TestTOMLComplexRegexPatterns(t *testing.T) {
+	// Create a temporary directory for testing
+	tmpDir, err := os.MkdirTemp("", "toml-complex-regex-test")
+	if err != nil {
+		t.Fatalf("Failed to create temp dir: %v", err)
+	}
+	defer os.RemoveAll(tmpDir)
+
+	// Create TOML content with complex regex patterns
+	tomlContent := `[[commands]]
+name = "ComplexPatterns"
+regexes = [
+    "\\[section\\.([^\\]]+)\\]",
+    "(?P<key>\\w+)\\s*=\\s*(?P<value>\\d+\\.\\d+)",
+    "network\\.(\\w+)\\.(enable|disable)"
+]
+lua = "if is_number(value) then value = num(value) * 1.1 end; return true"
+files = ["*.conf", "*.ini"]
+`
+
+	tomlFile := filepath.Join(tmpDir, "test.toml")
+	err = os.WriteFile(tomlFile, []byte(tomlContent), 0644)
+	if err != nil {
+		t.Fatalf("Failed to write TOML test file: %v", err)
+	}
+
+	// Change to temp directory
+	origDir, _ := os.Getwd()
+	defer os.Chdir(origDir)
+	os.Chdir(tmpDir)
+
+	// Test loading TOML commands
+	commands, _, err := utils.LoadCommandsFromTomlFiles("test.toml")
+	assert.NoError(t, err, "Should load TOML commands without error")
+	assert.Len(t, commands, 1, "Should load 1 command from TOML")
+
+	// Verify the complex regex command
+	cmd := commands[0]
+	assert.Equal(t, "ComplexPatterns", cmd.Name, "Command name should match")
+	assert.Len(t, cmd.Regexes, 3, "Should have 3 regex patterns")
+
+	// Verify each regex pattern
+	assert.Equal(t, `\[section\.([^\]]+)\]`, cmd.Regexes[0], "First regex should match section pattern")
+	assert.Equal(t, `(?P<key>\w+)\s*=\s*(?P<value>\d+\.\d+)`, cmd.Regexes[1], "Second regex should match key-value pattern")
+	assert.Equal(t, `network\.(\w+)\.(enable|disable)`, cmd.Regexes[2], "Third regex should match network pattern")
+
+	assert.Equal(t, []string{"*.conf", "*.ini"}, cmd.Files, "Files should match")
+}
+
+func TestTOMLJSONMode(t *testing.T) {
+	// Create a temporary directory for testing
+	tmpDir, err := os.MkdirTemp("", "toml-json-test")
+	if err != nil {
+		t.Fatalf("Failed to create temp dir: %v", err)
+	}
+	defer os.RemoveAll(tmpDir)
+
+	// Create TOML content with JSON mode commands
+	tomlContent := `[[commands]]
+name = "JSONMultiply"
+json = true
+lua = "for i, item in ipairs(data.items) do data.items[i].value = item.value * 2 end; return true"
+files = ["data.json"]
+
+[[commands]]
+name = "JSONObjectUpdate"
+json = true
+lua = "data.version = '2.0.0'; data.enabled = true; return true"
+files = ["config.json"]
+`
+
+	tomlFile := filepath.Join(tmpDir, "test.toml")
+	err = os.WriteFile(tomlFile, []byte(tomlContent), 0644)
+	if err != nil {
+		t.Fatalf("Failed to write TOML test file: %v", err)
+	}
+
+	// Change to temp directory
+	origDir, _ := os.Getwd()
+	defer os.Chdir(origDir)
+	os.Chdir(tmpDir)
+
+	// Test loading TOML commands
+	commands, _, err := utils.LoadCommandsFromTomlFiles("test.toml")
+	assert.NoError(t, err, "Should load TOML commands without error")
+	assert.Len(t, commands, 2, "Should load 2 commands from TOML")
+
+	// Verify first JSON command
+	cmd1 := commands[0]
+	assert.Equal(t, "JSONMultiply", cmd1.Name, "First command name should match")
+	assert.True(t, cmd1.JSON, "First command should have JSON mode enabled")
+	assert.Equal(t, "for i, item in ipairs(data.items) do data.items[i].value = item.value * 2 end; return true", cmd1.Lua, "First command Lua should match")
+	assert.Equal(t, []string{"data.json"}, cmd1.Files, "First command files should match")
+
+	// Verify second JSON command
+	cmd2 := commands[1]
+	assert.Equal(t, "JSONObjectUpdate", cmd2.Name, "Second command name should match")
+	assert.True(t, cmd2.JSON, "Second command should have JSON mode enabled")
+	assert.Equal(t, "data.version = '2.0.0'; data.enabled = true; return true", cmd2.Lua, "Second command Lua should match")
+	assert.Equal(t, []string{"config.json"}, cmd2.Files, "Second command files should match")
+}
+
+func TestTOMLEndToEndIntegration(t *testing.T) {
+	// Create a temporary directory for testing
+	tmpDir, err := os.MkdirTemp("", "toml-integration-test")
+	if err != nil {
+		t.Fatalf("Failed to create temp dir: %v", err)
+	}
+	defer os.RemoveAll(tmpDir)
+
+	// Create comprehensive TOML content
+	tomlContent := `[variables]
+multiplier = 4
+base_value = 100
+
+[[commands]]
+name = "IntegrationTest"
+regex = '''
+\[kinetics\.stressValues\.v2\.capacity\]
+
+    steam_engine = !num
+
+    water_wheel = !num
+
+    copper_valve_handle = !num'''
+lua = "v1 * multiplier"
+files = ["test.txt"]
+isolate = true
+
+[[commands]]
+name = "SimplePattern"
+regex = "enabled = (true|false)"
+lua = "= false"
+files = ["test.txt"]
+`
+
+	tomlFile := filepath.Join(tmpDir, "test.toml")
+	err = os.WriteFile(tomlFile, []byte(tomlContent), 0644)
+	if err != nil {
+		t.Fatalf("Failed to write TOML test file: %v", err)
+	}
+
+	// Create test file that matches the patterns
+	testContent := `[kinetics.stressValues.v2.capacity]
+
+    steam_engine = 256
+
+    water_wheel = 64
+
+    copper_valve_handle = 16
+
+some_other_setting = enabled = true
+`
+
+	testFile := filepath.Join(tmpDir, "test.txt")
+	err = os.WriteFile(testFile, []byte(testContent), 0644)
+	if err != nil {
+		t.Fatalf("Failed to write test file: %v", err)
+	}
+
+	// Change to temp directory
+	origDir, _ := os.Getwd()
+	defer os.Chdir(origDir)
+	os.Chdir(tmpDir)
+
+	// Test the complete workflow using the main function
+	commands, variables, err := utils.LoadCommands([]string{"test.toml"})
+	assert.NoError(t, err, "Should load TOML commands without error")
+	assert.Len(t, commands, 2, "Should load 2 commands")
+	assert.Len(t, variables, 2, "Should load 2 variables")
+
+	// Associate files with commands
+	files := []string{"test.txt"}
+	associations, err := utils.AssociateFilesWithCommands(files, commands)
+	assert.NoError(t, err, "Should associate files with commands")
+
+	// Verify associations
+	association := associations["test.txt"]
+	assert.Len(t, association.IsolateCommands, 1, "Should have 1 isolate command")
+	assert.Len(t, association.Commands, 1, "Should have 1 regular command")
+	assert.Equal(t, "IntegrationTest", association.IsolateCommands[0].Name, "Isolate command should match")
+	assert.Equal(t, "SimplePattern", association.Commands[0].Name, "Regular command should match")
+
+	t.Logf("TOML integration test completed successfully")
+	t.Logf("Loaded %d commands from TOML", len(commands))
+	t.Logf("Associated commands: %d isolate, %d regular",
+		len(association.IsolateCommands), len(association.Commands))
+}
+
+func TestTOMLErrorHandling(t *testing.T) {
+	// Create a temporary directory for testing
+	tmpDir, err := os.MkdirTemp("", "toml-error-test")
+	if err != nil {
+		t.Fatalf("Failed to create temp dir: %v", err)
+	}
+	defer os.RemoveAll(tmpDir)
+
+	// Change to temp directory
+	origDir, _ := os.Getwd()
+	defer os.Chdir(origDir)
+	os.Chdir(tmpDir)
+
+	// Test 1: Invalid TOML syntax
+	invalidTOML := `[[commands]]
+name = "Invalid"
+regex = "test = !num"
+lua = "v1 * 2"
+files = ["test.txt"
+# Missing closing bracket
+`
+
+	invalidFile := filepath.Join(tmpDir, "invalid.toml")
+	err = os.WriteFile(invalidFile, []byte(invalidTOML), 0644)
+	assert.NoError(t, err, "Should write invalid TOML file")
+
+	commands, _, err := utils.LoadCommandsFromTomlFiles("invalid.toml")
+	assert.Error(t, err, "Should return error for invalid TOML syntax")
+	assert.Nil(t, commands, "Should return nil commands for invalid TOML")
+	assert.Contains(t, err.Error(), "failed to unmarshal TOML file", "Error should mention TOML unmarshaling")
+
+	// Test 2: Non-existent file
+	commands, _, err = utils.LoadCommandsFromTomlFiles("nonexistent.toml")
+	assert.NoError(t, err, "Should handle non-existent file without error")
+	assert.Empty(t, commands, "Should return empty commands for non-existent file")
+
+	// Test 3: Empty TOML file returns no commands (not an error)
+	emptyFile := filepath.Join(tmpDir, "empty.toml")
+	err = os.WriteFile(emptyFile, []byte(""), 0644)
+	assert.NoError(t, err, "Should write empty TOML file")
+
+	commands, _, err = utils.LoadCommandsFromTomlFiles("empty.toml")
+	assert.NoError(t, err, "Empty TOML should not return error")
+	assert.Empty(t, commands, "Should return empty commands for empty TOML")
+}
+
+func TestYAMLToTOMLConversion(t *testing.T) {
+	// Create a temporary directory for testing
+	tmpDir, err := os.MkdirTemp("", "yaml-to-toml-conversion-test")
+	if err != nil {
+		t.Fatalf("Failed to create temp dir: %v", err)
+	}
+	defer os.RemoveAll(tmpDir)
+
+	// Change to temp directory
+	origDir, _ := os.Getwd()
+	defer os.Chdir(origDir)
+	os.Chdir(tmpDir)
+
+	// Create a test YAML file
+	yamlContent := `variables:
+  multiplier: 2.5
+  prefix: "CONV_"
+
+commands:
+  - name: "ConversionTest"
+    regex: "value = !num"
+    lua: "v1 * 3"
+    files: ["test.txt"]
+    loglevel: DEBUG
+  - name: "AnotherTest"
+    regex: "enabled = (true|false)"
+    lua: "= false"
+    files: ["*.conf"]
+`
+
+	yamlFile := filepath.Join(tmpDir, "test.yml")
+	err = os.WriteFile(yamlFile, []byte(yamlContent), 0644)
+	assert.NoError(t, err, "Should write YAML test file")
+
+	// Test conversion
+	err = utils.ConvertYAMLToTOML("test.yml")
+	assert.NoError(t, err, "Should convert YAML to TOML without error")
+
+	// Check that TOML file was created
+	tomlFile := filepath.Join(tmpDir, "test.toml")
+	_, err = os.Stat(tomlFile)
+	assert.NoError(t, err, "TOML file should exist after conversion")
+
+	// Read and verify TOML content
+	tomlData, err := os.ReadFile(tomlFile)
+	assert.NoError(t, err, "Should read TOML file")
+
+	tomlContent := string(tomlData)
+	assert.Contains(t, tomlContent, `name = "ConversionTest"`, "TOML should contain first command name")
+	assert.Contains(t, tomlContent, `name = "AnotherTest"`, "TOML should contain second command name")
+	assert.Contains(t, tomlContent, `[variables]`, "TOML should contain variables section")
+	assert.Contains(t, tomlContent, `multiplier = 2.5`, "TOML should contain multiplier")
+	assert.Contains(t, tomlContent, `prefix = "CONV_"`, "TOML should contain prefix")
+
+	// Test that converted TOML loads correctly
+	commands, variables, err := utils.LoadCommandsFromTomlFiles("test.toml")
+	assert.NoError(t, err, "Should load converted TOML without error")
+	assert.Len(t, commands, 2, "Should load 2 commands from converted TOML")
+	assert.Len(t, variables, 2, "Should have 2 variables")
+
+	// Variables are now loaded separately, not as part of commands
+
+	// Test skip functionality - run conversion again
+	err = utils.ConvertYAMLToTOML("test.yml")
+	assert.NoError(t, err, "Should handle existing TOML file without error")
+
+	// Verify original TOML file wasn't modified
+	originalTomlData, err := os.ReadFile(tomlFile)
+	assert.NoError(t, err, "Should read TOML file again")
+	assert.Equal(t, tomlData, originalTomlData, "TOML file content should be unchanged")
+
+	t.Logf("YAML to TOML conversion test completed successfully")
+}

utils/db.go

@@ -0,0 +1,162 @@
+package utils
+
+import (
+	"errors"
+	"path/filepath"
+	"time"
+
+	logger "git.site.quack-lab.dev/dave/cylogger"
+	"gorm.io/driver/sqlite"
+	"gorm.io/gorm"
+	gormlogger "gorm.io/gorm/logger"
+)
+
+// dbLogger is a scoped logger for the utils/db package.
+var dbLogger = logger.Default.WithPrefix("utils/db")
+
+type DB interface {
+	DB() *gorm.DB
+	Raw(sql string, args ...any) *gorm.DB
+	SaveFile(filePath string, fileData []byte) error
+	GetFile(filePath string) ([]byte, error)
+	GetAllFiles() ([]FileSnapshot, error)
+	RemoveAllFiles() error
+}
+
+type FileSnapshot struct {
+	Date     time.Time `gorm:"primaryKey"`
+	FilePath string    `gorm:"primaryKey"`
+	FileData []byte    `gorm:"type:blob"`
+}
+
+type DBWrapper struct {
+	db *gorm.DB
+}
+
+var globalDB *DBWrapper
+
+func GetDB() (DB, error) {
+	getDBLogger := dbLogger.WithPrefix("GetDB")
+	getDBLogger.Debug("Attempting to get database connection")
+	var err error
+
+	dbFile := filepath.Join("data.sqlite")
+	getDBLogger.Debug("Opening database file: %q", dbFile)
+	getDBLogger.Trace("Database configuration: PrepareStmt=true, GORM logger=Silent")
+	db, err := gorm.Open(sqlite.Open(dbFile), &gorm.Config{
+		// SkipDefaultTransaction: true,
+		PrepareStmt: true,
+		Logger:      gormlogger.Default.LogMode(gormlogger.Silent),
+	})
+	if err != nil {
+		getDBLogger.Error("Failed to open database file %q: %v", dbFile, err)
+		return nil, err
+	}
+	getDBLogger.Debug("Database opened successfully, running auto migration for FileSnapshot model")
+	if err := db.AutoMigrate(&FileSnapshot{}); err != nil {
+		getDBLogger.Error("Auto migration failed for FileSnapshot model: %v", err)
+		return nil, err
+	}
+	getDBLogger.Info("Database initialized and migrated successfully")
+
+	globalDB = &DBWrapper{db: db}
+	getDBLogger.Debug("Database wrapper initialized and cached globally")
+	return globalDB, nil
+}
+
+// Just a wrapper
+func (db *DBWrapper) Raw(sql string, args ...any) *gorm.DB {
+	rawLogger := dbLogger.WithPrefix("Raw").WithField("sql", sql)
+	rawLogger.Debug("Executing raw SQL query with args: %v", args)
+	return db.db.Raw(sql, args...)
+}
+
+func (db *DBWrapper) DB() *gorm.DB {
+	dbLogger.WithPrefix("DB").Debug("Returning GORM DB instance")
+	return db.db
+}
+
+func (db *DBWrapper) FileExists(filePath string) (bool, error) {
+	fileExistsLogger := dbLogger.WithPrefix("FileExists").WithField("filePath", filePath)
+	fileExistsLogger.Debug("Checking if file exists in database")
+	var count int64
+	err := db.db.Model(&FileSnapshot{}).Where("file_path = ?", filePath).Count(&count).Error
+	if err != nil {
+		fileExistsLogger.Error("Error checking if file exists: %v", err)
+		return false, err
+	}
+	fileExistsLogger.Debug("File exists: %t", count > 0)
+	return count > 0, err
+}
+
+func (db *DBWrapper) SaveFile(filePath string, fileData []byte) error {
+	saveFileLogger := dbLogger.WithPrefix("SaveFile").WithField("filePath", filePath).WithField("dataSize", len(fileData))
+	saveFileLogger.Debug("Attempting to save file to database")
+	saveFileLogger.Trace("File data length: %d", len(fileData))
+
+	exists, err := db.FileExists(filePath)
+	if err != nil {
+		saveFileLogger.Error("Error checking if file exists: %v", err)
+		return err
+	}
+	if exists {
+		saveFileLogger.Debug("File already exists in database, skipping save to avoid overwriting original snapshot")
+		return nil
+	}
+	saveFileLogger.Debug("Creating new file snapshot in database")
+	err = db.db.Create(&FileSnapshot{
+		Date:     time.Now(),
+		FilePath: filePath,
+		FileData: fileData,
+	}).Error
+	if err != nil {
+		saveFileLogger.Error("Failed to create file snapshot: %v", err)
+	} else {
+		saveFileLogger.Info("File successfully saved to database")
+	}
+	return err
+}
+
+func (db *DBWrapper) GetFile(filePath string) ([]byte, error) {
+	getFileLogger := dbLogger.WithPrefix("GetFile").WithField("filePath", filePath)
+	getFileLogger.Debug("Getting file from database")
+	var fileSnapshot FileSnapshot
+	err := db.db.Model(&FileSnapshot{}).Where("file_path = ?", filePath).First(&fileSnapshot).Error
+	if err != nil {
+		if errors.Is(err, gorm.ErrRecordNotFound) {
+			getFileLogger.Debug("File not found in database: %v", err)
+		} else {
+			getFileLogger.Warning("Failed to get file from database: %v", err)
+		}
+		return nil, err
+	}
+	getFileLogger.Debug("File found in database")
+	getFileLogger.Trace("Retrieved file data length: %d", len(fileSnapshot.FileData))
+	return fileSnapshot.FileData, nil
+}
+
+func (db *DBWrapper) GetAllFiles() ([]FileSnapshot, error) {
+	getAllFilesLogger := dbLogger.WithPrefix("GetAllFiles")
+	getAllFilesLogger.Debug("Getting all files from database")
+	var fileSnapshots []FileSnapshot
+	err := db.db.Model(&FileSnapshot{}).Find(&fileSnapshots).Error
+	if err != nil {
+		getAllFilesLogger.Error("Failed to get all files from database: %v", err)
+		return nil, err
+	}
+	getAllFilesLogger.Debug("Found %d files in database", len(fileSnapshots))
+	getAllFilesLogger.Trace("File snapshots retrieved: %v", fileSnapshots)
+	return fileSnapshots, nil
+}
+
+func (db *DBWrapper) RemoveAllFiles() error {
+	removeAllFilesLogger := dbLogger.WithPrefix("RemoveAllFiles")
+	removeAllFilesLogger.Debug("Removing all files from database")
+	err := db.db.Exec("DELETE FROM file_snapshots").Error
+	if err != nil {
+		removeAllFilesLogger.Error("Failed to remove all files from database: %v", err)
+	} else {
+		removeAllFilesLogger.Debug("All files removed from database")
+	}
+	return err
+}

utils/file.go

@@ -0,0 +1,106 @@
+package utils
+
+import (
+	"os"
+	"strings"
+
+	logger "git.site.quack-lab.dev/dave/cylogger"
+)
+
+// fileLogger is a scoped logger for the utils/file package.
+var fileLogger = logger.Default.WithPrefix("utils/file")
+
+// LimitString truncates a string to maxLen and adds "..." if truncated
+func LimitString(s string, maxLen int) string {
+	limitStringLogger := fileLogger.WithPrefix("LimitString").WithField("originalLength", len(s)).WithField("maxLength", maxLen)
+	limitStringLogger.Debug("Limiting string length")
+	s = strings.ReplaceAll(s, "\n", "\\n")
+	if len(s) <= maxLen {
+		limitStringLogger.Trace("String length (%d) is within max length (%d), no truncation", len(s), maxLen)
+		return s
+	}
+	limited := s[:maxLen-3] + "..."
+	limitStringLogger.Trace("String truncated from %d to %d characters: %q", len(s), len(limited), limited)
+	return limited
+}
+
+func ResetWhereNecessary(associations map[string]FileCommandAssociation, db DB) error {
+	resetWhereNecessaryLogger := fileLogger.WithPrefix("ResetWhereNecessary")
+	resetWhereNecessaryLogger.Debug("Starting reset where necessary operation")
+	resetWhereNecessaryLogger.Trace("File-command associations input: %v", associations)
+	dirtyFiles := make(map[string]struct{})
+	for _, association := range associations {
+		resetWhereNecessaryLogger.Debug("Processing association for file: %q", association.File)
+		for _, command := range association.Commands {
+			resetWhereNecessaryLogger.Debug("Checking command %q for reset requirement", command.Name)
+			resetWhereNecessaryLogger.Trace("Command details: %v", command)
+			if command.Reset {
+				resetWhereNecessaryLogger.Debug("Command %q requires reset for file %q, marking as dirty", command.Name, association.File)
+				dirtyFiles[association.File] = struct{}{}
+			}
+		}
+		for _, command := range association.IsolateCommands {
+			resetWhereNecessaryLogger.Debug("Checking isolate command %q for reset requirement", command.Name)
+			resetWhereNecessaryLogger.Trace("Isolate command details: %v", command)
+			if command.Reset {
+				resetWhereNecessaryLogger.Debug("Isolate command %q requires reset for file %q, marking as dirty", command.Name, association.File)
+				dirtyFiles[association.File] = struct{}{}
+			}
+		}
+	}
+	resetWhereNecessaryLogger.Debug("Identified %d files that need to be reset", len(dirtyFiles))
+	resetWhereNecessaryLogger.Trace("Dirty files identified: %v", dirtyFiles)
+
+	for file := range dirtyFiles {
+		resetWhereNecessaryLogger.Debug("Resetting file %q", file)
+		fileData, err := db.GetFile(file)
+		if err != nil {
+			resetWhereNecessaryLogger.Warning("Failed to get original content for file %q from database: %v", file, err)
+			// Seed the snapshot from current disk content if missing, then use it as fallback
+			currentData, readErr := os.ReadFile(file)
+			if readErr != nil {
+				resetWhereNecessaryLogger.Warning("Additionally failed to read current file content for %q: %v", file, readErr)
+				continue
+			}
+			// Best-effort attempt to save baseline; ignore errors to avoid blocking reset
+			if saveErr := db.SaveFile(file, currentData); saveErr != nil {
+				resetWhereNecessaryLogger.Warning("Failed to seed baseline snapshot for %q: %v", file, saveErr)
+			}
+			fileData = currentData
+		}
+		resetWhereNecessaryLogger.Trace("Retrieved original file data length for %q: %d", file, len(fileData))
+		resetWhereNecessaryLogger.Debug("Writing original content back to file %q", file)
+		err = os.WriteFile(file, fileData, 0644)
+		if err != nil {
+			resetWhereNecessaryLogger.Warning("Failed to write original content back to file %q: %v", file, err)
+			continue
+		}
+		resetWhereNecessaryLogger.Debug("Successfully reset file %q", file)
+	}
+	resetWhereNecessaryLogger.Debug("Finished reset where necessary operation")
+	return nil
+}
+
+func ResetAllFiles(db DB) error {
+	resetAllFilesLogger := fileLogger.WithPrefix("ResetAllFiles")
+	resetAllFilesLogger.Debug("Starting reset all files operation")
+	fileSnapshots, err := db.GetAllFiles()
+	if err != nil {
+		resetAllFilesLogger.Error("Failed to get all file snapshots from database: %v", err)
+		return err
+	}
+	resetAllFilesLogger.Debug("Found %d files in database to reset", len(fileSnapshots))
+	resetAllFilesLogger.Trace("File snapshots retrieved: %v", fileSnapshots)
+
+	for _, fileSnapshot := range fileSnapshots {
+		resetAllFilesLogger.Debug("Resetting file %q", fileSnapshot.FilePath)
+		err = os.WriteFile(fileSnapshot.FilePath, fileSnapshot.FileData, 0644)
+		if err != nil {
+			resetAllFilesLogger.Warning("Failed to write file %q to disk: %v", fileSnapshot.FilePath, err)
+			continue
+		}
+		resetAllFilesLogger.Debug("File %q written to disk successfully", fileSnapshot.FilePath)
+	}
+	resetAllFilesLogger.Debug("Finished reset all files operation")
+	return nil
+}

utils/file_test.go

@@ -0,0 +1,209 @@
+package utils
+
+import (
+	"os"
+	"path/filepath"
+	"testing"
+
+	"github.com/stretchr/testify/assert"
+)
+
+func TestLimitString(t *testing.T) {
+	tests := []struct {
+		name     string
+		input    string
+		maxLen   int
+		expected string
+	}{
+		{
+			name:     "Short string",
+			input:    "hello",
+			maxLen:   10,
+			expected: "hello",
+		},
+		{
+			name:     "Exact length",
+			input:    "hello",
+			maxLen:   5,
+			expected: "hello",
+		},
+		{
+			name:     "Too long",
+			input:    "hello world",
+			maxLen:   8,
+			expected: "hello...",
+		},
+		{
+			name:     "With newlines",
+			input:    "hello\nworld",
+			maxLen:   20,
+			expected: "hello\\nworld",
+		},
+		{
+			name:     "With newlines truncated",
+			input:    "hello\nworld\nfoo\nbar",
+			maxLen:   15,
+			expected: "hello\\nworld...",
+		},
+	}
+
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			result := LimitString(tt.input, tt.maxLen)
+			assert.Equal(t, tt.expected, result)
+		})
+	}
+}
+
+func TestResetWhereNecessary(t *testing.T) {
+	tmpDir, err := os.MkdirTemp("", "reset-test-*")
+	assert.NoError(t, err)
+	defer os.RemoveAll(tmpDir)
+
+	// Create test files
+	file1 := filepath.Join(tmpDir, "file1.txt")
+	file2 := filepath.Join(tmpDir, "file2.txt")
+	file3 := filepath.Join(tmpDir, "file3.txt")
+
+	err = os.WriteFile(file1, []byte("original1"), 0644)
+	assert.NoError(t, err)
+	err = os.WriteFile(file2, []byte("original2"), 0644)
+	assert.NoError(t, err)
+	err = os.WriteFile(file3, []byte("original3"), 0644)
+	assert.NoError(t, err)
+
+	// Modify files
+	err = os.WriteFile(file1, []byte("modified1"), 0644)
+	assert.NoError(t, err)
+	err = os.WriteFile(file2, []byte("modified2"), 0644)
+	assert.NoError(t, err)
+
+	// Create mock DB
+	db, err := GetDB()
+	assert.NoError(t, err)
+	err = db.SaveFile(file1, []byte("original1"))
+	assert.NoError(t, err)
+	err = db.SaveFile(file2, []byte("original2"))
+	assert.NoError(t, err)
+	// file3 not in DB
+
+	// Create associations with reset commands
+	associations := map[string]FileCommandAssociation{
+		file1: {
+			File: file1,
+			Commands: []ModifyCommand{
+				{Name: "cmd1", Reset: true},
+			},
+		},
+		file2: {
+			File: file2,
+			IsolateCommands: []ModifyCommand{
+				{Name: "cmd2", Reset: true},
+			},
+		},
+		file3: {
+			File: file3,
+			Commands: []ModifyCommand{
+				{Name: "cmd3", Reset: false}, // No reset
+			},
+		},
+	}
+
+	// Run reset
+	err = ResetWhereNecessary(associations, db)
+	assert.NoError(t, err)
+
+	// Verify file1 was reset
+	data, _ := os.ReadFile(file1)
+	assert.Equal(t, "original1", string(data))
+
+	// Verify file2 was reset
+	data, _ = os.ReadFile(file2)
+	assert.Equal(t, "original2", string(data))
+
+	// Verify file3 was NOT reset
+	data, _ = os.ReadFile(file3)
+	assert.Equal(t, "original3", string(data))
+}
+
+func TestResetWhereNecessaryMissingFromDB(t *testing.T) {
+	tmpDir, err := os.MkdirTemp("", "reset-missing-test-*")
+	assert.NoError(t, err)
+	defer os.RemoveAll(tmpDir)
+
+	// Create a test file that's been modified
+	file1 := filepath.Join(tmpDir, "file1.txt")
+	err = os.WriteFile(file1, []byte("modified_content"), 0644)
+	assert.NoError(t, err)
+
+	// Create DB but DON'T save file to it
+	db, err := GetDB()
+	assert.NoError(t, err)
+
+	// Create associations with reset command
+	associations := map[string]FileCommandAssociation{
+		file1: {
+			File: file1,
+			Commands: []ModifyCommand{
+				{Name: "cmd1", Reset: true},
+			},
+		},
+	}
+
+	// Run reset - should use current disk content as fallback
+	err = ResetWhereNecessary(associations, db)
+	assert.NoError(t, err)
+
+	// Verify file was "reset" to current content (saved to DB for next time)
+	data, _ := os.ReadFile(file1)
+	assert.Equal(t, "modified_content", string(data))
+
+	// Verify it was saved to DB
+	savedData, err := db.GetFile(file1)
+	assert.NoError(t, err)
+	assert.Equal(t, "modified_content", string(savedData))
+}
+
+func TestResetAllFiles(t *testing.T) {
+	tmpDir, err := os.MkdirTemp("", "reset-all-test-*")
+	assert.NoError(t, err)
+	defer os.RemoveAll(tmpDir)
+
+	// Create test files
+	file1 := filepath.Join(tmpDir, "file1.txt")
+	file2 := filepath.Join(tmpDir, "file2.txt")
+
+	err = os.WriteFile(file1, []byte("original1"), 0644)
+	assert.NoError(t, err)
+	err = os.WriteFile(file2, []byte("original2"), 0644)
+	assert.NoError(t, err)
+
+	// Create mock DB and save originals
+	db, err := GetDB()
+	assert.NoError(t, err)
+	err = db.SaveFile(file1, []byte("original1"))
+	assert.NoError(t, err)
+	err = db.SaveFile(file2, []byte("original2"))
+	assert.NoError(t, err)
+
+	// Modify files
+	err = os.WriteFile(file1, []byte("modified1"), 0644)
+	assert.NoError(t, err)
+	err = os.WriteFile(file2, []byte("modified2"), 0644)
+	assert.NoError(t, err)
+
+	// Verify they're modified
+	data, _ := os.ReadFile(file1)
+	assert.Equal(t, "modified1", string(data))
+
+	// Reset all
+	err = ResetAllFiles(db)
+	assert.NoError(t, err)
+
+	// Verify both were reset
+	data, _ = os.ReadFile(file1)
+	assert.Equal(t, "original1", string(data))
+
+	data, _ = os.ReadFile(file2)
+	assert.Equal(t, "original2", string(data))
+}

utils/flags.go

@@ -1,15 +0,0 @@
-package utils
-
-import (
-	"flag"
-)
-
-var (
-	// Deprecated
-	GitFlag       = flag.Bool("git", false, "Use git to manage files")
-	// Deprecated
-	ResetFlag     = flag.Bool("reset", false, "Reset files to their original state")
-	LogLevel      = flag.String("loglevel", "INFO", "Set log level: ERROR, WARNING, INFO, DEBUG, TRACE")
-	Cookfile      = flag.String("cook", "**/cook.yml", "Path to cook config files, can be globbed")
-	ParallelFiles = flag.Int("P", 100, "Number of files to process in parallel")
-)

utils/git.go

@@ -1,97 +0,0 @@
-package utils
-
-import (
-	"fmt"
-	"modify/logger"
-	"os"
-	"path/filepath"
-	"time"
-
-	"github.com/go-git/go-git/v5/plumbing/object"
-	"github.com/go-git/go-git/v5"
-)
-
-var (
-	Repo     *git.Repository
-	Worktree *git.Worktree
-)
-
-func SetupGit() error {
-	cwd, err := os.Getwd()
-	if err != nil {
-		return fmt.Errorf("failed to get current working directory: %w", err)
-	}
-	logger.Debug("Current working directory obtained: %s", cwd)
-
-	logger.Debug("Attempting to open git repository at %s", cwd)
-	Repo, err = git.PlainOpen(cwd)
-	if err != nil {
-		logger.Debug("No existing git repository found at %s, attempting to initialize a new git repository.", cwd)
-		Repo, err = git.PlainInit(cwd, false)
-		if err != nil {
-			return fmt.Errorf("failed to initialize a new git repository at %s: %w", cwd, err)
-		}
-		logger.Info("Successfully initialized a new git repository at %s", cwd)
-	} else {
-		logger.Info("Successfully opened existing git repository at %s", cwd)
-	}
-
-	logger.Debug("Attempting to obtain worktree for repository at %s", cwd)
-	Worktree, err = Repo.Worktree()
-	if err != nil {
-		return fmt.Errorf("failed to obtain worktree for repository at %s: %w", cwd, err)
-	}
-	logger.Debug("Successfully obtained worktree for repository at %s", cwd)
-	return nil
-}
-
-func CleanupGitFiles(files []string) error {
-	for _, file := range files {
-		logger.Debug("Checking git status for file: %s", file)
-		status, err := Worktree.Status()
-		if err != nil {
-			logger.Error("Error getting worktree status: %v", err)
-			fmt.Fprintf(os.Stderr, "Error getting worktree status: %v\n", err)
-			return fmt.Errorf("error getting worktree status: %w", err)
-		}
-		if status.IsUntracked(file) {
-			logger.Info("Detected untracked file: %s. Adding to git index.", file)
-			_, err = Worktree.Add(file)
-			if err != nil {
-				logger.Error("Error adding file to git: %v", err)
-				fmt.Fprintf(os.Stderr, "Error adding file to git: %v\n", err)
-				return fmt.Errorf("error adding file to git: %w", err)
-			}
-
-			filename := filepath.Base(file)
-			logger.Info("File %s added successfully. Committing with message: 'Track %s'", filename, filename)
-			_, err = Worktree.Commit("Track "+filename, &git.CommitOptions{
-				Author: &object.Signature{
-					Name:  "Big Chef",
-					Email: "bigchef@bigchef.com",
-					When:  time.Now(),
-				},
-			})
-			if err != nil {
-				logger.Error("Error committing file: %v", err)
-				fmt.Fprintf(os.Stderr, "Error committing file: %v\n", err)
-				return fmt.Errorf("error committing file: %w", err)
-			}
-			logger.Info("Successfully committed file: %s", filename)
-		} else {
-			logger.Info("File %s is already tracked. Restoring it to the working tree.", file)
-			err := Worktree.Restore(&git.RestoreOptions{
-				Files:    []string{file},
-				Staged:   true,
-				Worktree: true,
-			})
-			if err != nil {
-				logger.Error("Error restoring file: %v", err)
-				fmt.Fprintf(os.Stderr, "Error restoring file: %v\n", err)
-				return fmt.Errorf("error restoring file: %w", err)
-			}
-			logger.Info("File %s restored successfully", file)
-		}
-	}
-	return nil
-}

utils/modifycommand.go

@@ -2,207 +2,590 @@ package utils
 
 import (
 	"fmt"
-	"modify/logger"
 	"os"
+	"path/filepath"
+	"strings"
 
+	logger "git.site.quack-lab.dev/dave/cylogger"
+	"github.com/BurntSushi/toml"
 	"github.com/bmatcuk/doublestar/v4"
 	"gopkg.in/yaml.v3"
 )
 
+// modifyCommandLogger is a scoped logger for the utils/modifycommand package.
+var modifyCommandLogger = logger.Default.WithPrefix("utils/modifycommand")
+
 type ModifyCommand struct {
-	Name     string   `yaml:"name"`
-	Regex    string   `yaml:"regex"`
-	Lua      string   `yaml:"lua"`
-	Files    []string `yaml:"files"`
-	Git      bool     `yaml:"git"`
-	Reset    bool     `yaml:"reset"`
-	LogLevel string   `yaml:"loglevel"`
+	Name      string   `yaml:"name,omitempty" toml:"name,omitempty"`
+	Regex     string   `yaml:"regex,omitempty" toml:"regex,omitempty"`
+	Regexes   []string `yaml:"regexes,omitempty" toml:"regexes,omitempty"`
+	Lua       string   `yaml:"lua,omitempty" toml:"lua,omitempty"`
+	Files     []string `yaml:"files,omitempty" toml:"files,omitempty"`
+	Reset     bool     `yaml:"reset,omitempty" toml:"reset,omitempty"`
+	LogLevel  string   `yaml:"loglevel,omitempty" toml:"loglevel,omitempty"`
+	Isolate   bool     `yaml:"isolate,omitempty" toml:"isolate,omitempty"`
+	NoDedup   bool     `yaml:"nodedup,omitempty" toml:"nodedup,omitempty"`
+	Disabled  bool     `yaml:"disable,omitempty" toml:"disable,omitempty"`
+	JSON      bool     `yaml:"json,omitempty" toml:"json,omitempty"`
+	SourceDir string   `yaml:"-" toml:"-"` // Directory of the config file that loaded this command
 }
+
 type CookFile []ModifyCommand
 
 func (c *ModifyCommand) Validate() error {
-	if c.Regex == "" {
-		return fmt.Errorf("pattern is required")
+	validateLogger := modifyCommandLogger.WithPrefix("Validate").WithField("commandName", c.Name)
+	validateLogger.Debug("Validating command")
+
+	// For JSON mode, regex patterns are not required
+	if !c.JSON {
+		if c.Regex == "" && len(c.Regexes) == 0 {
+			validateLogger.Error("Validation failed: Regex pattern is required for non-JSON mode")
+			return fmt.Errorf("pattern is required for non-JSON mode")
+		}
 	}
+
 	if c.Lua == "" {
+		validateLogger.Error("Validation failed: Lua expression is required")
 		return fmt.Errorf("lua expression is required")
 	}
 	if len(c.Files) == 0 {
+		validateLogger.Error("Validation failed: At least one file is required")
 		return fmt.Errorf("at least one file is required")
 	}
 	if c.LogLevel == "" {
+		validateLogger.Debug("LogLevel not specified, defaulting to INFO")
 		c.LogLevel = "INFO"
 	}
+	validateLogger.Debug("Command validated successfully")
 	return nil
 }
 
-func AssociateFilesWithCommands(files []string, commands []ModifyCommand) (map[string][]ModifyCommand, error) {
+// Ehh.. Not much better... Guess this wasn't the big deal
+var matchesMemoTable map[string]bool = make(map[string]bool)
+var globMemoTable map[string][]string = make(map[string][]string)
+
+func Matches(path string, glob string) (bool, error) {
+	matchesLogger := modifyCommandLogger.WithPrefix("Matches").WithField("path", path).WithField("glob", glob)
+	matchesLogger.Debug("Checking if path matches glob")
+	key := fmt.Sprintf("%s:%s", path, glob)
+	if matches, ok := matchesMemoTable[key]; ok {
+		matchesLogger.Debug("Found match in memo table: %t", matches)
+		return matches, nil
+	}
+	matches, err := doublestar.Match(glob, path)
+	if err != nil {
+		matchesLogger.Error("Failed to match glob: %v", err)
+		return false, fmt.Errorf("failed to match glob %s with file %s: %w", glob, path, err)
+	}
+	matchesMemoTable[key] = matches
+	matchesLogger.Debug("Match result: %t, storing in memo table", matches)
+	return matches, nil
+}
+
+func SplitPattern(pattern string) (string, string) {
+	splitPatternLogger := modifyCommandLogger.WithPrefix("SplitPattern").WithField("pattern", pattern)
+	splitPatternLogger.Debug("Splitting pattern")
+	splitPatternLogger.Trace("Original pattern: %q", pattern)
+
+	// Split the pattern first to separate static and wildcard parts
+	static, remainingPattern := doublestar.SplitPattern(pattern)
+	splitPatternLogger.Trace("After split: static=%q, pattern=%q", static, remainingPattern)
+
+	// Resolve the static part to handle ~ expansion and make it absolute
+	// ResolvePath already normalizes to forward slashes
+	static = ResolvePath(static)
+	splitPatternLogger.Trace("Resolved static part: %q", static)
+
+	splitPatternLogger.Trace("Final static path: %q, Remaining pattern: %q", static, remainingPattern)
+	return static, remainingPattern
+}
+
+type FileCommandAssociation struct {
+	File            string
+	IsolateCommands []ModifyCommand
+	Commands        []ModifyCommand
+}
+
+func AssociateFilesWithCommands(files []string, commands []ModifyCommand) (map[string]FileCommandAssociation, error) {
+	associateFilesLogger := modifyCommandLogger.WithPrefix("AssociateFilesWithCommands")
+	associateFilesLogger.Debug("Associating files with commands")
+	associateFilesLogger.Trace("Input files: %v", files)
+	associateFilesLogger.Trace("Input commands: %v", commands)
 	associationCount := 0
-	fileCommands := make(map[string][]ModifyCommand)
+	fileCommands := make(map[string]FileCommandAssociation)
+
 	for _, file := range files {
+		// Use centralized path resolution internally but keep original file as key
+		resolvedFile := ResolvePath(file)
+		associateFilesLogger.Debug("Processing file: %q (resolved: %q)", file, resolvedFile)
+		fileCommands[file] = FileCommandAssociation{
+			File:            resolvedFile,
+			IsolateCommands: []ModifyCommand{},
+			Commands:        []ModifyCommand{},
+		}
 		for _, command := range commands {
+			associateFilesLogger.Debug("Checking command %q for file %q", command.Name, file)
 			for _, glob := range command.Files {
-				// TODO: Maybe memoize this function call
-				matches, err := doublestar.Match(glob, file)
+				// SplitPattern now handles tilde expansion and path resolution
+				static, pattern := SplitPattern(glob)
+				associateFilesLogger.Trace("Glob parts for %q → static=%q pattern=%q", glob, static, pattern)
+
+				// Use resolved file for matching (already normalized to forward slashes by ResolvePath)
+				absFile := resolvedFile
+				associateFilesLogger.Trace("Absolute file path resolved for matching: %q", absFile)
+
+				// Only match if the file is under the static root
+				if !(strings.HasPrefix(absFile, static+"/") || absFile == static) {
+					associateFilesLogger.Trace("Skipping glob %q for file %q because file is outside static root %q", glob, file, static)
+					continue
+				}
+
+				patternFile := strings.TrimPrefix(absFile, static+`/`)
+				associateFilesLogger.Trace("Pattern-relative path used for match: %q", patternFile)
+				matches, err := Matches(patternFile, pattern)
 				if err != nil {
-					logger.Trace("Failed to match glob %s with file %s: %v", glob, file, err)
+					associateFilesLogger.Warning("Failed to match glob %q with file %q: %v", glob, file, err)
 					continue
 				}
 				if matches {
-					logger.Debug("Found match for file %q and command %q", file, command.Regex)
-					fileCommands[file] = append(fileCommands[file], command)
+					associateFilesLogger.Debug("File %q matches glob %q. Associating with command %q", file, glob, command.Name)
+					association := fileCommands[file]
+
+					if command.Isolate {
+						associateFilesLogger.Debug("Command %q is an isolate command, adding to isolate list", command.Name)
+						association.IsolateCommands = append(association.IsolateCommands, command)
+					} else {
+						associateFilesLogger.Debug("Command %q is a regular command, adding to regular list", command.Name)
+						association.Commands = append(association.Commands, command)
+					}
+					fileCommands[file] = association
 					associationCount++
+				} else {
+					associateFilesLogger.Trace("File %q did not match glob %q (pattern=%q, rel=%q)", file, glob, pattern, patternFile)
 				}
 			}
 		}
-		logger.Debug("Found %d commands for file %q", len(fileCommands[file]), file)
-		if len(fileCommands[file]) == 0 {
-			logger.Info("No commands found for file %q", file)
-		}
+		currentFileCommands := fileCommands[file]
+		associateFilesLogger.Debug("Finished processing file %q. Found %d regular commands and %d isolate commands", file, len(currentFileCommands.Commands), len(currentFileCommands.IsolateCommands))
+		associateFilesLogger.Trace("Commands for file %q: %v", file, currentFileCommands.Commands)
+		associateFilesLogger.Trace("Isolate commands for file %q: %v", file, currentFileCommands.IsolateCommands)
 	}
-	logger.Info("Found %d associations between %d files and %d commands", associationCount, len(files), len(commands))
+	associateFilesLogger.Info("Completed association. Found %d total associations for %d files and %d commands", associationCount, len(files), len(commands))
 	return fileCommands, nil
 }
 
 func AggregateGlobs(commands []ModifyCommand) map[string]struct{} {
-	logger.Info("Aggregating globs for %d commands", len(commands))
+	aggregateGlobsLogger := modifyCommandLogger.WithPrefix("AggregateGlobs")
+	aggregateGlobsLogger.Debug("Aggregating glob patterns from commands")
+	aggregateGlobsLogger.Trace("Input commands for aggregation: %v", commands)
 	globs := make(map[string]struct{})
 	for _, command := range commands {
+		aggregateGlobsLogger.Debug("Processing command %q for glob patterns", command.Name)
 		for _, glob := range command.Files {
-			globs[glob] = struct{}{}
+			// Split the glob into static and pattern parts, then resolve ONLY the static part
+			static, pattern := SplitPattern(glob)
+			// Reconstruct the glob with resolved static part
+			resolvedGlob := static
+			if pattern != "" {
+				resolvedGlob += "/" + pattern
+			}
+			aggregateGlobsLogger.Trace("Adding glob: %q (resolved to %q) [static=%s, pattern=%s]", glob, resolvedGlob, static, pattern)
+			globs[resolvedGlob] = struct{}{}
 		}
 	}
-	logger.Info("Found %d unique globs", len(globs))
+	aggregateGlobsLogger.Debug("Finished aggregating globs. Found %d unique glob patterns", len(globs))
+	aggregateGlobsLogger.Trace("Aggregated unique globs: %v", globs)
 	return globs
 }
 
-func ExpandGLobs(patterns map[string]struct{}) ([]string, error) {
+func ExpandGlobs(patterns map[string]struct{}) ([]string, error) {
+	expandGlobsLogger := modifyCommandLogger.WithPrefix("ExpandGLobs")
+	expandGlobsLogger.Debug("Expanding glob patterns to actual files")
+	expandGlobsLogger.Trace("Input patterns for expansion: %v", patterns)
 	var files []string
 	filesMap := make(map[string]bool)
 
 	cwd, err := os.Getwd()
 	if err != nil {
+		expandGlobsLogger.Error("Failed to get current working directory: %v", err)
 		return nil, fmt.Errorf("failed to get current working directory: %w", err)
 	}
+	expandGlobsLogger.Debug("Current working directory: %q", cwd)
 
-	logger.Debug("Expanding patterns from directory: %s", cwd)
 	for pattern := range patterns {
-		logger.Trace("Processing pattern: %s", pattern)
-		matches, _ := doublestar.Glob(os.DirFS(cwd), pattern)
-		logger.Debug("Found %d matches for pattern %s", len(matches), pattern)
-		for _, m := range matches {
-			info, err := os.Stat(m)
+		expandGlobsLogger.Debug("Processing glob pattern: %q", pattern)
+		static, pattern := SplitPattern(pattern)
+		key := static + "|" + pattern
+		matches, ok := globMemoTable[key]
+		if !ok {
+			var err error
+			matches, err = doublestar.Glob(os.DirFS(static), pattern)
 			if err != nil {
-				logger.Warning("Error getting file info for %s: %v", m, err)
+				expandGlobsLogger.Warning("Error expanding glob %q in %q: %v", pattern, static, err)
 				continue
 			}
-			if !info.IsDir() && !filesMap[m] {
-				logger.Trace("Adding file to process list: %s", m)
-				filesMap[m], files = true, append(files, m)
+			globMemoTable[key] = matches
+		}
+		expandGlobsLogger.Debug("Found %d matches for pattern %q", len(matches), pattern)
+		expandGlobsLogger.Trace("Raw matches for pattern %q: %v", pattern, matches)
+		for _, m := range matches {
+			// Resolve the full path
+			fullPath := ResolvePath(filepath.Join(static, m))
+			info, err := os.Stat(fullPath)
+			if err != nil {
+				expandGlobsLogger.Warning("Error getting file info for %q: %v", fullPath, err)
+				continue
+			}
+			if !info.IsDir() && !filesMap[fullPath] {
+				expandGlobsLogger.Trace("Adding unique file to list: %q", fullPath)
+				filesMap[fullPath], files = true, append(files, fullPath)
 			}
 		}
 	}
 
 	if len(files) > 0 {
-		logger.Debug("Found %d files to process: %v", len(files), files)
+		expandGlobsLogger.Debug("Finished expanding globs. Found %d unique files to process", len(files))
+		expandGlobsLogger.Trace("Unique files to process: %v", files)
+	} else {
+		expandGlobsLogger.Warning("No files found after expanding glob patterns.")
 	}
 	return files, nil
 }
 
-func LoadCommands(args []string) ([]ModifyCommand, error) {
+func LoadCommands(args []string) ([]ModifyCommand, map[string]interface{}, error) {
+	loadCommandsLogger := modifyCommandLogger.WithPrefix("LoadCommands")
+	loadCommandsLogger.Debug("Loading commands from arguments (cook files or direct patterns)")
+	loadCommandsLogger.Trace("Input arguments: %v", args)
 	commands := []ModifyCommand{}
+	variables := make(map[string]interface{})
 
-	logger.Info("Loading commands from cook files: %s", *Cookfile)
-	newcommands, err := LoadCommandsFromCookFiles(*Cookfile)
-	if err != nil {
-		return nil, fmt.Errorf("failed to load commands from cook files: %w", err)
-	}
-	logger.Info("Successfully loaded %d commands from cook files", len(newcommands))
-	commands = append(commands, newcommands...)
-	logger.Info("Now total commands: %d", len(commands))
+	for _, arg := range args {
+		loadCommandsLogger.Debug("Processing argument for commands: %q", arg)
+		var newCommands []ModifyCommand
+		var newVariables map[string]interface{}
+		var err error
 
-	logger.Info("Loading commands from arguments: %v", args)
-	newcommands, err = LoadCommandFromArgs(args)
-	if err != nil {
-		if len(commands) == 0 {
-			return nil, fmt.Errorf("failed to load commands from args: %w", err)
+		// Check file extension to determine format
+		if strings.HasSuffix(arg, ".toml") {
+			loadCommandsLogger.Debug("Loading TOML commands from %q", arg)
+			newCommands, newVariables, err = LoadCommandsFromTomlFiles(arg)
+			if err != nil {
+				loadCommandsLogger.Error("Failed to load TOML commands from argument %q: %v", arg, err)
+				return nil, nil, fmt.Errorf("failed to load commands from TOML files: %w", err)
+			}
+		} else {
+			// Default to YAML for .yml, .yaml, or any other extension
+			loadCommandsLogger.Debug("Loading YAML commands from %q", arg)
+			newCommands, newVariables, err = LoadCommandsFromCookFiles(arg)
+			if err != nil {
+				loadCommandsLogger.Error("Failed to load YAML commands from argument %q: %v", arg, err)
+				return nil, nil, fmt.Errorf("failed to load commands from cook files: %w", err)
+			}
+		}
+		for k, v := range newVariables {
+			variables[k] = v
 		}
-		logger.Warning("Failed to load commands from args: %v", err)
-	}
-	logger.Info("Successfully loaded %d commands from args", len(newcommands))
-	commands = append(commands, newcommands...)
-	logger.Info("Now total commands: %d", len(commands))
 
-	return commands, nil
+		loadCommandsLogger.Debug("Successfully loaded %d commands from %q", len(newCommands), arg)
+		for _, cmd := range newCommands {
+			if cmd.Disabled {
+				loadCommandsLogger.Debug("Skipping disabled command: %q", cmd.Name)
+				continue
+			}
+			commands = append(commands, cmd)
+			loadCommandsLogger.Trace("Added command %q. Current total commands: %d", cmd.Name, len(commands))
+		}
+	}
+
+	loadCommandsLogger.Info("Finished loading commands. Total %d commands and %d variables loaded", len(commands), len(variables))
+	return commands, variables, nil
 }
 
-func LoadCommandFromArgs(args []string) ([]ModifyCommand, error) {
-	// Cannot reset without git, right?
-	if *ResetFlag {
-		*GitFlag = true
-	}
-
-	if len(args) < 3 {
-		return nil, fmt.Errorf("at least %d arguments are required", 3)
-	}
-
-	command := ModifyCommand{
-		Regex:    args[0],
-		Lua:      args[1],
-		Files:    args[2:],
-		Git:      *GitFlag,
-		Reset:    *ResetFlag,
-		LogLevel: *LogLevel,
-	}
-
-	if err := command.Validate(); err != nil {
-		return nil, fmt.Errorf("invalid command: %w", err)
-	}
-
-	return []ModifyCommand{command}, nil
-}
-
-func LoadCommandsFromCookFiles(s string) ([]ModifyCommand, error) {
-	cwd, err := os.Getwd()
-	if err != nil {
-		return nil, fmt.Errorf("failed to get current working directory: %w", err)
-	}
-
+func LoadCommandsFromCookFiles(pattern string) ([]ModifyCommand, map[string]interface{}, error) {
+	loadCookFilesLogger := modifyCommandLogger.WithPrefix("LoadCommandsFromCookFiles").WithField("pattern", pattern)
+	loadCookFilesLogger.Debug("Loading commands from cook files based on pattern")
+	loadCookFilesLogger.Trace("Input pattern: %q", pattern)
+	static, pattern := SplitPattern(pattern)
 	commands := []ModifyCommand{}
-	cookFiles, err := doublestar.Glob(os.DirFS(cwd), *Cookfile)
+	variables := make(map[string]interface{})
+	cookFiles, err := doublestar.Glob(os.DirFS(static), pattern)
 	if err != nil {
-		return nil, fmt.Errorf("failed to glob cook files: %w", err)
+		loadCookFilesLogger.Error("Failed to glob cook files for pattern %q: %v", pattern, err)
+		return nil, nil, fmt.Errorf("failed to glob cook files: %w", err)
 	}
+	loadCookFilesLogger.Debug("Found %d cook files for pattern %q", len(cookFiles), pattern)
+	loadCookFilesLogger.Trace("Cook files found: %v", cookFiles)
 
 	for _, cookFile := range cookFiles {
+		// Use centralized path resolution
+		cookFile = ResolvePath(filepath.Join(static, cookFile))
+		loadCookFilesLogger.Debug("Loading commands from individual cook file: %q", cookFile)
+
 		cookFileData, err := os.ReadFile(cookFile)
 		if err != nil {
-			return nil, fmt.Errorf("failed to read cook file: %w", err)
+			loadCookFilesLogger.Error("Failed to read cook file %q: %v", cookFile, err)
+			return nil, nil, fmt.Errorf("failed to read cook file: %w", err)
 		}
-		newcommands, err := LoadCommandsFromCookFile(cookFileData)
+		loadCookFilesLogger.Trace("Read %d bytes from cook file %q", len(cookFileData), cookFile)
+		newCommands, newVariables, err := LoadCommandsFromCookFile(cookFileData)
 		if err != nil {
-			return nil, fmt.Errorf("failed to load commands from cook file: %w", err)
+			loadCookFilesLogger.Error("Failed to load commands from cook file data for %q: %v", cookFile, err)
+			return nil, nil, fmt.Errorf("failed to load commands from cook file: %w", err)
 		}
-		commands = append(commands, newcommands...)
+		// Set source directory for each command
+		sourceDir := filepath.Dir(cookFile)
+		for i := range newCommands {
+			newCommands[i].SourceDir = sourceDir
+		}
+		commands = append(commands, newCommands...)
+		for k, v := range newVariables {
+			variables[k] = v
+		}
+		loadCookFilesLogger.Debug("Added %d commands and %d variables from cook file %q. Total commands now: %d", len(newCommands), len(newVariables), cookFile, len(commands))
 	}
 
-	return commands, nil
+	loadCookFilesLogger.Debug("Finished loading commands from cook files. Total %d commands and %d variables", len(commands), len(variables))
+	return commands, variables, nil
 }
 
-func LoadCommandsFromCookFile(cookFileData []byte) ([]ModifyCommand, error) {
-	commands := []ModifyCommand{}
-	err := yaml.Unmarshal(cookFileData, &commands)
-	if err != nil {
-		return nil, fmt.Errorf("failed to unmarshal cook file: %w", err)
+func LoadCommandsFromCookFile(cookFileData []byte) ([]ModifyCommand, map[string]interface{}, error) {
+	loadCommandLogger := modifyCommandLogger.WithPrefix("LoadCommandsFromCookFile")
+	loadCommandLogger.Debug("Unmarshaling commands from cook file data")
+	loadCommandLogger.Trace("Cook file data length: %d", len(cookFileData))
+
+	var cookFile struct {
+		Variables map[string]interface{} `yaml:"variables,omitempty"`
+		Commands  []ModifyCommand        `yaml:"commands"`
 	}
-	return commands, nil
+
+	err := yaml.Unmarshal(cookFileData, &cookFile)
+	if err != nil {
+		loadCommandLogger.Error("Failed to unmarshal cook file data: %v", err)
+		return nil, nil, fmt.Errorf("failed to unmarshal cook file: %w", err)
+	}
+	loadCommandLogger.Debug("Successfully unmarshaled %d commands and %d variables", len(cookFile.Commands), len(cookFile.Variables))
+	loadCommandLogger.Trace("Unmarshaled commands: %v", cookFile.Commands)
+	loadCommandLogger.Trace("Unmarshaled variables: %v", cookFile.Variables)
+	return cookFile.Commands, cookFile.Variables, nil
 }
 
 // CountGlobsBeforeDedup counts the total number of glob patterns across all commands before deduplication
 func CountGlobsBeforeDedup(commands []ModifyCommand) int {
+	countGlobsLogger := modifyCommandLogger.WithPrefix("CountGlobsBeforeDedup")
+	countGlobsLogger.Debug("Counting glob patterns before deduplication")
 	count := 0
 	for _, cmd := range commands {
+		countGlobsLogger.Trace("Processing command %q, adding %d globs", cmd.Name, len(cmd.Files))
 		count += len(cmd.Files)
 	}
+	countGlobsLogger.Debug("Total glob patterns before deduplication: %d", count)
 	return count
 }
+
+func FilterCommands(commands []ModifyCommand, filter string) []ModifyCommand {
+	filterCommandsLogger := modifyCommandLogger.WithPrefix("FilterCommands").WithField("filter", filter)
+	filterCommandsLogger.Debug("Filtering commands")
+	filterCommandsLogger.Trace("Input commands: %v", commands)
+	filteredCommands := []ModifyCommand{}
+	filters := strings.Split(filter, ",")
+	filterCommandsLogger.Trace("Split filters: %v", filters)
+	for _, cmd := range commands {
+		filterCommandsLogger.Debug("Checking command %q against filters", cmd.Name)
+		for _, f := range filters {
+			if strings.Contains(cmd.Name, f) {
+				filterCommandsLogger.Debug("Command %q matches filter %q, adding to filtered list", cmd.Name, f)
+				filteredCommands = append(filteredCommands, cmd)
+				break // Command matches, no need to check other filters
+			}
+		}
+	}
+	filterCommandsLogger.Debug("Finished filtering commands. Found %d filtered commands", len(filteredCommands))
+	filterCommandsLogger.Trace("Filtered commands: %v", filteredCommands)
+	return filteredCommands
+}
+
+func LoadCommandsFromTomlFiles(pattern string) ([]ModifyCommand, map[string]interface{}, error) {
+	loadTomlFilesLogger := modifyCommandLogger.WithPrefix("LoadCommandsFromTomlFiles").WithField("pattern", pattern)
+	loadTomlFilesLogger.Debug("Loading commands from TOML files based on pattern")
+	loadTomlFilesLogger.Trace("Input pattern: %q", pattern)
+	static, pattern := SplitPattern(pattern)
+	commands := []ModifyCommand{}
+	variables := make(map[string]interface{})
+	tomlFiles, err := doublestar.Glob(os.DirFS(static), pattern)
+	if err != nil {
+		loadTomlFilesLogger.Error("Failed to glob TOML files for pattern %q: %v", pattern, err)
+		return nil, nil, fmt.Errorf("failed to glob TOML files: %w", err)
+	}
+	loadTomlFilesLogger.Debug("Found %d TOML files for pattern %q", len(tomlFiles), pattern)
+	loadTomlFilesLogger.Trace("TOML files found: %v", tomlFiles)
+
+	for _, tomlFile := range tomlFiles {
+		// Use centralized path resolution
+		tomlFile = ResolvePath(filepath.Join(static, tomlFile))
+		loadTomlFilesLogger.Debug("Loading commands from individual TOML file: %q", tomlFile)
+
+		tomlFileData, err := os.ReadFile(tomlFile)
+		if err != nil {
+			loadTomlFilesLogger.Error("Failed to read TOML file %q: %v", tomlFile, err)
+			return nil, nil, fmt.Errorf("failed to read TOML file: %w", err)
+		}
+		loadTomlFilesLogger.Trace("Read %d bytes from TOML file %q", len(tomlFileData), tomlFile)
+		newCommands, newVariables, err := LoadCommandsFromTomlFile(tomlFileData)
+		if err != nil {
+			loadTomlFilesLogger.Error("Failed to load commands from TOML file data for %q: %v", tomlFile, err)
+			return nil, nil, fmt.Errorf("failed to load commands from TOML file: %w", err)
+		}
+		// Set source directory for each command
+		sourceDir := filepath.Dir(tomlFile)
+		for i := range newCommands {
+			newCommands[i].SourceDir = sourceDir
+		}
+		commands = append(commands, newCommands...)
+		for k, v := range newVariables {
+			variables[k] = v
+		}
+		loadTomlFilesLogger.Debug("Added %d commands and %d variables from TOML file %q. Total commands now: %d", len(newCommands), len(newVariables), tomlFile, len(commands))
+	}
+
+	loadTomlFilesLogger.Debug("Finished loading commands from TOML files. Total %d commands and %d variables", len(commands), len(variables))
+	return commands, variables, nil
+}
+
+func LoadCommandsFromTomlFile(tomlFileData []byte) ([]ModifyCommand, map[string]interface{}, error) {
+	loadTomlCommandLogger := modifyCommandLogger.WithPrefix("LoadCommandsFromTomlFile")
+	loadTomlCommandLogger.Debug("Unmarshaling commands from TOML file data")
+	loadTomlCommandLogger.Trace("TOML file data length: %d", len(tomlFileData))
+
+	// TOML structure for commands array and top-level variables
+	var tomlData struct {
+		Variables map[string]interface{} `toml:"variables,omitempty"`
+		Commands  []ModifyCommand        `toml:"commands"`
+		// Also support direct array without wrapper
+		DirectCommands []ModifyCommand `toml:"-"`
+	}
+
+	// First try to parse as wrapped structure
+	err := toml.Unmarshal(tomlFileData, &tomlData)
+	if err != nil {
+		loadTomlCommandLogger.Error("Failed to unmarshal TOML file data: %v", err)
+		return nil, nil, fmt.Errorf("failed to unmarshal TOML file: %w", err)
+	}
+
+	var commands []ModifyCommand
+	variables := make(map[string]interface{})
+
+	// Extract top-level variables
+	if len(tomlData.Variables) > 0 {
+		loadTomlCommandLogger.Debug("Found %d top-level variables", len(tomlData.Variables))
+		for k, v := range tomlData.Variables {
+			variables[k] = v
+		}
+	}
+
+	// Use commands from wrapped structure
+	commands = tomlData.Commands
+	loadTomlCommandLogger.Debug("Successfully unmarshaled %d commands and %d variables", len(commands), len(variables))
+	loadTomlCommandLogger.Trace("Unmarshaled commands: %v", commands)
+	loadTomlCommandLogger.Trace("Unmarshaled variables: %v", variables)
+	return commands, variables, nil
+}
+
+// ConvertYAMLToTOML converts YAML files to TOML format
+func ConvertYAMLToTOML(yamlPattern string) error {
+	convertLogger := modifyCommandLogger.WithPrefix("ConvertYAMLToTOML").WithField("pattern", yamlPattern)
+	convertLogger.Debug("Starting YAML to TOML conversion")
+
+	// Find all YAML files matching the pattern
+	static, pattern := SplitPattern(yamlPattern)
+	yamlFiles, err := doublestar.Glob(os.DirFS(static), pattern)
+	if err != nil {
+		convertLogger.Error("Failed to glob YAML files: %v", err)
+		return fmt.Errorf("failed to glob YAML files: %w", err)
+	}
+
+	convertLogger.Debug("Found %d YAML files to convert", len(yamlFiles))
+
+	if len(yamlFiles) == 0 {
+		convertLogger.Info("No YAML files found for pattern: %s", yamlPattern)
+		return nil
+	}
+
+	conversionCount := 0
+	skippedCount := 0
+
+	for _, yamlFile := range yamlFiles {
+		// Use centralized path resolution
+		yamlFilePath := ResolvePath(filepath.Join(static, yamlFile))
+
+		// Generate corresponding TOML file path
+		tomlFilePath := strings.TrimSuffix(yamlFilePath, filepath.Ext(yamlFilePath)) + ".toml"
+
+		convertLogger.Debug("Processing YAML file: %s -> %s", yamlFilePath, tomlFilePath)
+
+		// Check if TOML file already exists
+		if _, err := os.Stat(tomlFilePath); err == nil {
+			convertLogger.Info("Skipping conversion - TOML file already exists: %s", tomlFilePath)
+			skippedCount++
+			continue
+		}
+
+		// Read YAML file
+		yamlData, err := os.ReadFile(yamlFilePath)
+		if err != nil {
+			convertLogger.Error("Failed to read YAML file %s: %v", yamlFilePath, err)
+			continue
+		}
+
+		// Load YAML commands from this specific file
+		fileCommands, fileVariables, err := LoadCommandsFromCookFile(yamlData)
+		if err != nil {
+			convertLogger.Error("Failed to parse YAML file %s: %v", yamlFilePath, err)
+			continue
+		}
+
+		// Convert to TOML structure
+		tomlData, err := convertCommandsToTOML(fileCommands, fileVariables)
+		if err != nil {
+			convertLogger.Error("Failed to convert commands to TOML for %s: %v", yamlFilePath, err)
+			continue
+		}
+
+		// Write TOML file
+		err = os.WriteFile(tomlFilePath, tomlData, 0644)
+		if err != nil {
+			convertLogger.Error("Failed to write TOML file %s: %v", tomlFilePath, err)
+			continue
+		}
+
+		convertLogger.Info("Successfully converted %s to %s", yamlFilePath, tomlFilePath)
+		conversionCount++
+	}
+
+	convertLogger.Info("Conversion completed: %d files converted, %d files skipped", conversionCount, skippedCount)
+	return nil
+}
+
+// convertCommandsToTOML converts a slice of ModifyCommand to TOML format
+func convertCommandsToTOML(commands []ModifyCommand, variables map[string]interface{}) ([]byte, error) {
+	convertLogger := modifyCommandLogger.WithPrefix("convertCommandsToTOML")
+	convertLogger.Debug("Converting %d commands to TOML format", len(commands))
+
+	// Create TOML structure
+	tomlData := struct {
+		Variables map[string]interface{} `toml:"variables,omitempty"`
+		Commands  []ModifyCommand        `toml:"commands"`
+	}{
+		Variables: variables,
+		Commands:  commands,
+	}
+
+	// Marshal to TOML
+	tomlBytes, err := toml.Marshal(tomlData)
+	if err != nil {
+		convertLogger.Error("Failed to marshal commands to TOML: %v", err)
+		return nil, fmt.Errorf("failed to marshal commands to TOML: %w", err)
+	}
+
+	convertLogger.Debug("Successfully converted %d commands and %d variables to TOML (%d bytes)", len(commands), len(variables), len(tomlBytes))
+	return tomlBytes, nil
+}

utils/modifycommand_coverage_test.go

@@ -0,0 +1,313 @@
+package utils
+
+import (
+	"os"
+	"path/filepath"
+	"testing"
+
+	"github.com/stretchr/testify/assert"
+)
+
+func TestAggregateGlobsWithDuplicates(t *testing.T) {
+	commands := []ModifyCommand{
+		{Files: []string{"*.txt", "*.md"}},
+		{Files: []string{"*.txt", "*.go"}}, // *.txt is duplicate
+		{Files: []string{"test/**/*.xml"}},
+	}
+
+	globs := AggregateGlobs(commands)
+
+	// Should deduplicate
+	assert.Equal(t, 4, len(globs))
+	// AggregateGlobs resolves paths, which uses forward slashes internally
+	assert.Contains(t, globs, ResolvePath("*.txt"))
+	assert.Contains(t, globs, ResolvePath("*.md"))
+	assert.Contains(t, globs, ResolvePath("*.go"))
+	assert.Contains(t, globs, ResolvePath("test/**/*.xml"))
+}
+
+func TestExpandGlobsWithActualFiles(t *testing.T) {
+	// Create temp dir with test files
+	tmpDir, err := os.MkdirTemp("", "glob-test-*")
+	assert.NoError(t, err)
+	defer os.RemoveAll(tmpDir)
+
+	// Create test files
+	testFile1 := filepath.Join(tmpDir, "test1.txt")
+	testFile2 := filepath.Join(tmpDir, "test2.txt")
+	testFile3 := filepath.Join(tmpDir, "test.md")
+
+	os.WriteFile(testFile1, []byte("test"), 0644)
+	os.WriteFile(testFile2, []byte("test"), 0644)
+	os.WriteFile(testFile3, []byte("test"), 0644)
+
+	// Change to temp directory so glob pattern can find files
+	origDir, _ := os.Getwd()
+	defer os.Chdir(origDir)
+	os.Chdir(tmpDir)
+
+	// Test expanding globs using ResolvePath to normalize the pattern
+	globs := map[string]struct{}{
+		ResolvePath("*.txt"): {},
+	}
+
+	files, err := ExpandGlobs(globs)
+	assert.NoError(t, err)
+	assert.Equal(t, 2, len(files))
+}
+
+func TestSplitPatternWithTilde(t *testing.T) {
+	pattern := "~/test/*.txt"
+	static, pat := SplitPattern(pattern)
+
+	// Should expand ~
+	assert.NotEqual(t, "~", static)
+	assert.Contains(t, pat, "*.txt")
+}
+
+func TestLoadCommandsWithDisabled(t *testing.T) {
+	tmpDir, err := os.MkdirTemp("", "disabled-test-*")
+	assert.NoError(t, err)
+	defer os.RemoveAll(tmpDir)
+
+	yamlContent := `
+variables:
+  test: "value"
+
+commands:
+  - name: "enabled_cmd"
+    regex: "test"
+    lua: "v1 * 2"
+    files: ["*.txt"]
+  - name: "disabled_cmd"
+    regex: "test2"
+    lua: "v1 * 3"
+    files: ["*.txt"]
+    disable: true
+`
+
+	yamlFile := filepath.Join(tmpDir, "test.yml")
+	err = os.WriteFile(yamlFile, []byte(yamlContent), 0644)
+	assert.NoError(t, err)
+
+	// Change to temp directory so LoadCommands can find the file with a simple pattern
+	origDir, _ := os.Getwd()
+	defer os.Chdir(origDir)
+	os.Chdir(tmpDir)
+
+	commands, variables, err := LoadCommands([]string{"test.yml"})
+	assert.NoError(t, err)
+
+	// Should only load enabled command
+	assert.Equal(t, 1, len(commands))
+	assert.Equal(t, "enabled_cmd", commands[0].Name)
+
+	// Should still load variables
+	assert.Equal(t, 1, len(variables))
+}
+
+func TestFilterCommandsByName(t *testing.T) {
+	commands := []ModifyCommand{
+		{Name: "test_multiply"},
+		{Name: "test_divide"},
+		{Name: "other_command"},
+		{Name: "test_add"},
+	}
+
+	// Filter by "test"
+	filtered := FilterCommands(commands, "test")
+	assert.Equal(t, 3, len(filtered))
+
+	// Filter by multiple
+	filtered = FilterCommands(commands, "multiply,divide")
+	assert.Equal(t, 2, len(filtered))
+}
+
+func TestCountGlobsBeforeDedup(t *testing.T) {
+	commands := []ModifyCommand{
+		{Files: []string{"*.txt", "*.md", "*.go"}},
+		{Files: []string{"*.xml"}},
+		{Files: []string{"test/**/*.txt", "data/**/*.json"}},
+	}
+
+	count := CountGlobsBeforeDedup(commands)
+	assert.Equal(t, 6, count)
+}
+
+func TestMatchesWithMemoization(t *testing.T) {
+	path := "test/file.txt"
+	glob := "**/*.txt"
+
+	// First call
+	matches1, err1 := Matches(path, glob)
+	assert.NoError(t, err1)
+	assert.True(t, matches1)
+
+	// Second call should use memo
+	matches2, err2 := Matches(path, glob)
+	assert.NoError(t, err2)
+	assert.Equal(t, matches1, matches2)
+}
+
+func TestValidateCommand(t *testing.T) {
+	tests := []struct {
+		name    string
+		cmd     ModifyCommand
+		wantErr bool
+	}{
+		{
+			name: "Valid command",
+			cmd: ModifyCommand{
+				Regex: "test",
+				Lua:   "v1 * 2",
+				Files: []string{"*.txt"},
+			},
+			wantErr: false,
+		},
+		{
+			name: "Valid JSON mode without regex",
+			cmd: ModifyCommand{
+				JSON:  true,
+				Lua:   "data.value = data.value * 2; modified = true",
+				Files: []string{"*.json"},
+			},
+			wantErr: false,
+		},
+		{
+			name: "Missing regex in non-JSON mode",
+			cmd: ModifyCommand{
+				Lua:   "v1 * 2",
+				Files: []string{"*.txt"},
+			},
+			wantErr: true,
+		},
+		{
+			name: "Missing Lua",
+			cmd: ModifyCommand{
+				Regex: "test",
+				Files: []string{"*.txt"},
+			},
+			wantErr: true,
+		},
+		{
+			name: "Missing files",
+			cmd: ModifyCommand{
+				Regex: "test",
+				Lua:   "v1 * 2",
+			},
+			wantErr: true,
+		},
+	}
+
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			err := tt.cmd.Validate()
+			if tt.wantErr {
+				assert.Error(t, err)
+			} else {
+				assert.NoError(t, err)
+			}
+		})
+	}
+}
+
+func TestLoadCommandsFromTomlWithVariables(t *testing.T) {
+	tmpDir, err := os.MkdirTemp("", "toml-vars-test-*")
+	assert.NoError(t, err)
+	defer os.RemoveAll(tmpDir)
+
+	tomlContent := `[variables]
+multiplier = 3
+prefix = "PREFIX_"
+
+[[commands]]
+name = "test_cmd"
+regex = "value = !num"
+lua = "v1 * multiplier"
+files = ["*.txt"]
+`
+
+	tomlFile := filepath.Join(tmpDir, "test.toml")
+	err = os.WriteFile(tomlFile, []byte(tomlContent), 0644)
+	assert.NoError(t, err)
+
+	// Change to temp directory so glob pattern can find the file
+	origDir, _ := os.Getwd()
+	defer os.Chdir(origDir)
+	os.Chdir(tmpDir)
+
+	commands, variables, err := LoadCommandsFromTomlFiles("test.toml")
+	assert.NoError(t, err)
+	assert.Equal(t, 1, len(commands))
+	assert.Equal(t, 2, len(variables))
+	assert.Equal(t, int64(3), variables["multiplier"])
+	assert.Equal(t, "PREFIX_", variables["prefix"])
+}
+
+func TestConvertYAMLToTOMLSkipExisting(t *testing.T) {
+	tmpDir, err := os.MkdirTemp("", "convert-skip-test-*")
+	assert.NoError(t, err)
+	defer os.RemoveAll(tmpDir)
+
+	// Create YAML file
+	yamlContent := `
+commands:
+  - name: "test"
+    regex: "value"
+    lua: "v1 * 2"
+    files: ["*.txt"]
+`
+	yamlFile := filepath.Join(tmpDir, "test.yml")
+	err = os.WriteFile(yamlFile, []byte(yamlContent), 0644)
+	assert.NoError(t, err)
+
+	// Create TOML file (should skip conversion)
+	tomlFile := filepath.Join(tmpDir, "test.toml")
+	err = os.WriteFile(tomlFile, []byte("# existing"), 0644)
+	assert.NoError(t, err)
+
+	// Change to temp dir
+	origDir, _ := os.Getwd()
+	defer os.Chdir(origDir)
+	os.Chdir(tmpDir)
+
+	// Should skip existing TOML
+	err = ConvertYAMLToTOML("test.yml")
+	assert.NoError(t, err)
+
+	// TOML content should be unchanged
+	content, _ := os.ReadFile(tomlFile)
+	assert.Equal(t, "# existing", string(content))
+}
+
+func TestLoadCommandsWithTomlExtension(t *testing.T) {
+	tmpDir, err := os.MkdirTemp("", "toml-ext-test-*")
+	assert.NoError(t, err)
+	defer os.RemoveAll(tmpDir)
+
+	tomlContent := `
+[variables]
+test_var = "value"
+
+[[commands]]
+name = "TestCmd"
+regex = "test"
+lua = "return true"
+files = ["*.txt"]
+`
+	tomlFile := filepath.Join(tmpDir, "test.toml")
+	err = os.WriteFile(tomlFile, []byte(tomlContent), 0644)
+	assert.NoError(t, err)
+
+	origDir, _ := os.Getwd()
+	defer os.Chdir(origDir)
+	os.Chdir(tmpDir)
+
+	// This should trigger the .toml suffix check in LoadCommands
+	commands, variables, err := LoadCommands([]string{"test.toml"})
+	assert.NoError(t, err)
+	assert.Len(t, commands, 1)
+	assert.Equal(t, "TestCmd", commands[0].Name)
+	assert.Len(t, variables, 1)
+	assert.Equal(t, "value", variables["test_var"])
+}

utils/modifycommand_test.go

@@ -158,21 +158,24 @@ func TestAssociateFilesWithCommands(t *testing.T) {
 
 	// The associations expected depends on the implementation
 	// Let's check the actual associations and verify they make sense
-	for file, cmds := range associations {
-		t.Logf("File %s is associated with %d commands", file, len(cmds))
-		for i, cmd := range cmds {
+	for file, assoc := range associations {
+		t.Logf("File %s is associated with %d commands and %d isolate commands", file, len(assoc.Commands), len(assoc.IsolateCommands))
+		for i, cmd := range assoc.Commands {
 			t.Logf("  Command %d: Pattern=%s, Files=%v", i, cmd.Regex, cmd.Files)
 		}
+		for i, cmd := range assoc.IsolateCommands {
+			t.Logf("  Isolate Command %d: Pattern=%s, Files=%v", i, cmd.Regex, cmd.Files)
+		}
 
 		// Specific validation based on our file types
 		switch file {
 		case "file1.xml":
-			if len(cmds) < 1 {
-				t.Errorf("Expected at least 1 command for file1.xml, got %d", len(cmds))
+			if len(assoc.Commands) < 1 {
+				t.Errorf("Expected at least 1 command for file1.xml, got %d", len(assoc.Commands))
 			}
 			// Verify at least one command with *.xml pattern
 			hasXmlGlob := false
-			for _, cmd := range cmds {
+			for _, cmd := range assoc.Commands {
 				for _, glob := range cmd.Files {
 					if glob == "*.xml" {
 						hasXmlGlob = true
@@ -187,12 +190,12 @@ func TestAssociateFilesWithCommands(t *testing.T) {
 				t.Errorf("Expected command with *.xml glob for file1.xml")
 			}
 		case "file2.txt":
-			if len(cmds) < 1 {
-				t.Errorf("Expected at least 1 command for file2.txt, got %d", len(cmds))
+			if len(assoc.Commands) < 1 {
+				t.Errorf("Expected at least 1 command for file2.txt, got %d", len(assoc.Commands))
 			}
 			// Verify at least one command with *.txt pattern
 			hasTxtGlob := false
-			for _, cmd := range cmds {
+			for _, cmd := range assoc.Commands {
 				for _, glob := range cmd.Files {
 					if glob == "*.txt" {
 						hasTxtGlob = true
@@ -207,12 +210,12 @@ func TestAssociateFilesWithCommands(t *testing.T) {
 				t.Errorf("Expected command with *.txt glob for file2.txt")
 			}
 		case "subdir/file3.xml":
-			if len(cmds) < 1 {
-				t.Errorf("Expected at least 1 command for subdir/file3.xml, got %d", len(cmds))
+			if len(assoc.Commands) < 1 {
+				t.Errorf("Expected at least 1 command for subdir/file3.xml, got %d", len(assoc.Commands))
 			}
 			// Should match both *.xml and subdir/* patterns
 			matches := 0
-			for _, cmd := range cmds {
+			for _, cmd := range assoc.Commands {
 				for _, glob := range cmd.Files {
 					if glob == "*.xml" || glob == "subdir/*" {
 						matches++
@@ -248,11 +251,19 @@ func TestAggregateGlobs(t *testing.T) {
 
 	globs := AggregateGlobs(commands)
 
+	// Now we properly resolve only the static part of globs
+	// *.xml has no static part (current dir), so it becomes resolved_dir/*.xml
+	// *.txt has no static part (current dir), so it becomes resolved_dir/*.txt
+	// *.json has no static part (current dir), so it becomes resolved_dir/*.json
+	// subdir/*.xml has static "subdir", so it becomes resolved_dir/subdir/*.xml
+	cwd, _ := os.Getwd()
+	resolvedCwd := ResolvePath(cwd)
+
 	expected := map[string]struct{}{
-		"*.xml":        {},
-		"*.txt":        {},
-		"*.json":       {},
-		"subdir/*.xml": {},
+		resolvedCwd + "/*.xml":        {},
+		resolvedCwd + "/*.txt":        {},
+		resolvedCwd + "/*.json":       {},
+		resolvedCwd + "/subdir/*.xml": {},
 	}
 
 	if len(globs) != len(expected) {
@@ -266,142 +277,21 @@ func TestAggregateGlobs(t *testing.T) {
 	}
 }
 
-func TestLoadCommandFromArgs(t *testing.T) {
-	// Save original flags
-	origGitFlag := *GitFlag
-	origResetFlag := *ResetFlag
-	origLogLevel := *LogLevel
-
-	// Restore original flags after test
-	defer func() {
-		*GitFlag = origGitFlag
-		*ResetFlag = origResetFlag
-		*LogLevel = origLogLevel
-	}()
-
-	// Test cases
-	tests := []struct {
-		name        string
-		args        []string
-		gitFlag     bool
-		resetFlag   bool
-		logLevel    string
-		shouldError bool
-	}{
-		{
-			name:        "Valid command",
-			args:        []string{"pattern", "expr", "file1", "file2"},
-			gitFlag:     false,
-			resetFlag:   false,
-			logLevel:    "INFO",
-			shouldError: false,
-		},
-		{
-			name:        "Not enough args",
-			args:        []string{"pattern", "expr"},
-			gitFlag:     false,
-			resetFlag:   false,
-			logLevel:    "INFO",
-			shouldError: true,
-		},
-		{
-			name:        "With git flag",
-			args:        []string{"pattern", "expr", "file1"},
-			gitFlag:     true,
-			resetFlag:   false,
-			logLevel:    "INFO",
-			shouldError: false,
-		},
-		{
-			name:        "With reset flag (forces git flag)",
-			args:        []string{"pattern", "expr", "file1"},
-			gitFlag:     false,
-			resetFlag:   true,
-			logLevel:    "INFO",
-			shouldError: false,
-		},
-		{
-			name:        "With custom log level",
-			args:        []string{"pattern", "expr", "file1"},
-			gitFlag:     false,
-			resetFlag:   false,
-			logLevel:    "DEBUG",
-			shouldError: false,
-		},
-	}
-
-	for _, tc := range tests {
-		t.Run(tc.name, func(t *testing.T) {
-			// Set flags for this test case
-			*GitFlag = tc.gitFlag
-			*ResetFlag = tc.resetFlag
-			*LogLevel = tc.logLevel
-
-			commands, err := LoadCommandFromArgs(tc.args)
-
-			if tc.shouldError {
-				if err == nil {
-					t.Errorf("Expected an error but got none")
-				}
-				return
-			}
-
-			if err != nil {
-				t.Errorf("Unexpected error: %v", err)
-				return
-			}
-
-			if len(commands) != 1 {
-				t.Errorf("Expected 1 command, got %d", len(commands))
-				return
-			}
-
-			cmd := commands[0]
-
-			// Check command properties
-			if cmd.Regex != tc.args[0] {
-				t.Errorf("Expected pattern %q, got %q", tc.args[0], cmd.Regex)
-			}
-
-			if cmd.Lua != tc.args[1] {
-				t.Errorf("Expected LuaExpr %q, got %q", tc.args[1], cmd.Lua)
-			}
-
-			if len(cmd.Files) != len(tc.args)-2 {
-				t.Errorf("Expected %d files, got %d", len(tc.args)-2, len(cmd.Files))
-			}
-
-			// When reset is true, git should be true regardless of what was set
-			expectedGit := tc.gitFlag || tc.resetFlag
-			if cmd.Git != expectedGit {
-				t.Errorf("Expected Git flag %v, got %v", expectedGit, cmd.Git)
-			}
-
-			if cmd.Reset != tc.resetFlag {
-				t.Errorf("Expected Reset flag %v, got %v", tc.resetFlag, cmd.Reset)
-			}
-
-			if cmd.LogLevel != tc.logLevel {
-				t.Errorf("Expected LogLevel %q, got %q", tc.logLevel, cmd.LogLevel)
-			}
-		})
-	}
-}
-
 // Successfully unmarshal valid YAML data into ModifyCommand slice
 func TestLoadCommandsFromCookFileSuccess(t *testing.T) {
 	// Arrange
 	yamlData := []byte(`
-- name: command1
-  pattern: "*.txt"
-  lua: replace
-- name: command2
-  pattern: "*.go"
-  lua: delete
+commands:
+  - name: command1
+    regex: "*.txt"
+    lua: replace
+  - name: command2
+    regex: "*.go"
+    lua: delete
 `)
 
 	// Act
-	commands, err := LoadCommandsFromCookFile(yamlData)
+	commands, _, err := LoadCommandsFromCookFile(yamlData)
 
 	// Assert
 	assert.NoError(t, err)
@@ -419,17 +309,18 @@ func TestLoadCommandsFromCookFileWithComments(t *testing.T) {
 	// Arrange
 	yamlData := []byte(`
     # This is a comment
-    - name: command1
-      pattern: "*.txt"
-      lua: replace
-    # Another comment
-    - name: command2
-      pattern: "*.go"
-      lua: delete
+    commands:
+      - name: command1
+        regex: "*.txt"
+        lua: replace
+      # Another comment
+      - name: command2
+        regex: "*.go"
+        lua: delete
     `)
 
 	// Act
-	commands, err := LoadCommandsFromCookFile(yamlData)
+	commands, _, err := LoadCommandsFromCookFile(yamlData)
 
 	// Assert
 	assert.NoError(t, err)
@@ -445,10 +336,10 @@ func TestLoadCommandsFromCookFileWithComments(t *testing.T) {
 // Handle different YAML formatting styles (flow vs block)
 func TestLoadCommandsFromCookFileWithFlowStyle(t *testing.T) {
 	// Arrange
-	yamlData := []byte(`[ { name: command1, pattern: "*.txt", lua: replace }, { name: command2, pattern: "*.go", lua: delete } ]`)
+	yamlData := []byte(`commands: [ { name: command1, regex: "*.txt", lua: replace }, { name: command2, regex: "*.go", lua: delete } ]`)
 
 	// Act
-	commands, err := LoadCommandsFromCookFile(yamlData)
+	commands, _, err := LoadCommandsFromCookFile(yamlData)
 
 	// Assert
 	assert.NoError(t, err)
@@ -468,8 +359,8 @@ func TestLoadCommandsFromCookFileNilOrEmptyData(t *testing.T) {
 	emptyData := []byte{}
 
 	// Act
-	commandsNil, errNil := LoadCommandsFromCookFile(nilData)
-	commandsEmpty, errEmpty := LoadCommandsFromCookFile(emptyData)
+	commandsNil, _, errNil := LoadCommandsFromCookFile(nilData)
+	commandsEmpty, _, errEmpty := LoadCommandsFromCookFile(emptyData)
 
 	// Assert
 	assert.Nil(t, errNil)
@@ -484,7 +375,7 @@ func TestLoadCommandsFromCookFileEmptyData(t *testing.T) {
 	yamlData := []byte(``)
 
 	// Act
-	commands, err := LoadCommandsFromCookFile(yamlData)
+	commands, _, err := LoadCommandsFromCookFile(yamlData)
 
 	// Assert
 	assert.NoError(t, err)
@@ -495,19 +386,20 @@ func TestLoadCommandsFromCookFileEmptyData(t *testing.T) {
 func TestLoadCommandsFromCookFileWithMultipleEntries(t *testing.T) {
 	// Arrange
 	yamlData := []byte(`
-- name: command1
-  pattern: "*.txt"
-  lua: replace
-- name: command2
-  pattern: "*.go"
-  lua: delete
-- name: command3
-  pattern: "*.md"
-  lua: append
+commands:
+  - name: command1
+    regex: "*.txt"
+    lua: replace
+  - name: command2
+    regex: "*.go"
+    lua: delete
+  - name: command3
+    regex: "*.md"
+    lua: append
 `)
 
 	// Act
-	commands, err := LoadCommandsFromCookFile(yamlData)
+	commands, _, err := LoadCommandsFromCookFile(yamlData)
 
 	// Assert
 	assert.NoError(t, err)
@@ -526,26 +418,27 @@ func TestLoadCommandsFromCookFileWithMultipleEntries(t *testing.T) {
 func TestLoadCommandsFromCookFileLegitExample(t *testing.T) {
 	// Arrange
 	yamlData := []byte(`
-- name: crewlayabout
-  pattern: '<Talent identifier="crewlayabout">!anyvalue="(?<repairspeedpenalty>!num)"!anyvalue="(?<skillpenalty>!num)"!anyvalue="(?<repairspeedbonus>!num)"!anyvalue="(?<skillbonus>!num)"!anydistance="(?<distance>!num)"!anySkillBonus!anyvalue="(?<skillpenaltyv>!num)"!anyvalue="(?<skillpenaltyv1>!num)"!anyvalue="(?<skillpenaltyv2>!num)"!anyvalue="(?<skillpenaltyv3>!num)"!anyvalue="(?<skillpenaltyv4>!num)"!anyvalue="(?<repairspeedpenaltyv>!num)'
-  lua: |
-    repairspeedpenalty=round(repairspeedpenalty/2, 2)
-    skillpenalty=round(skillpenalty/2, 0)
-    repairspeedbonus=round(repairspeedbonus*2, 2)
-    skillbonus=round(skillbonus*2, 0)
-    distance=round(distance*2, 0)
-    skillpenaltyv=skillpenalty
-    skillpenaltyv1=skillpenalty
-    skillpenaltyv2=skillpenalty
-    skillpenaltyv3=skillpenalty
-    skillpenaltyv4=skillpenalty
-    repairspeedpenaltyv=round(-repairspeedpenalty/100, 2)
-  files:
-    - '**/TalentsAssistant.xml'
+commands:
+  - name: crewlayabout
+    pattern: '<Talent identifier="crewlayabout">!anyvalue="(?<repairspeedpenalty>!num)"!anyvalue="(?<skillpenalty>!num)"!anyvalue="(?<repairspeedbonus>!num)"!anyvalue="(?<skillbonus>!num)"!anydistance="(?<distance>!num)"!anySkillBonus!anyvalue="(?<skillpenaltyv>!num)"!anyvalue="(?<skillpenaltyv1>!num)"!anyvalue="(?<skillpenaltyv2>!num)"!anyvalue="(?<skillpenaltyv3>!num)"!anyvalue="(?<skillpenaltyv4>!num)"!anyvalue="(?<repairspeedpenaltyv>!num)'
+    lua: |
+      repairspeedpenalty=round(repairspeedpenalty/2, 2)
+      skillpenalty=round(skillpenalty/2, 0)
+      repairspeedbonus=round(repairspeedbonus*2, 2)
+      skillbonus=round(skillbonus*2, 0)
+      distance=round(distance*2, 0)
+      skillpenaltyv=skillpenalty
+      skillpenaltyv1=skillpenalty
+      skillpenaltyv2=skillpenalty
+      skillpenaltyv3=skillpenalty
+      skillpenaltyv4=skillpenalty
+      repairspeedpenaltyv=round(-repairspeedpenalty/100, 2)
+    files:
+      - '**/TalentsAssistant.xml'
 `)
 
 	// Act
-	commands, err := LoadCommandsFromCookFile(yamlData)
+	commands, _, err := LoadCommandsFromCookFile(yamlData)
 
 	// Assert
 	assert.NoError(t, err)
@@ -553,155 +446,6 @@ func TestLoadCommandsFromCookFileLegitExample(t *testing.T) {
 	assert.Equal(t, "crewlayabout", commands[0].Name)
 }
 
-// Valid command with minimum 3 arguments returns a ModifyCommand slice with correct values
-func TestLoadCommandFromArgsWithValidArguments(t *testing.T) {
-	// Setup
-	oldGitFlag := GitFlag
-	oldResetFlag := ResetFlag
-	oldLogLevel := LogLevel
-
-	gitValue := true
-	resetValue := false
-	logLevelValue := "info"
-
-	GitFlag = &gitValue
-	ResetFlag = &resetValue
-	LogLevel = &logLevelValue
-
-	defer func() {
-		GitFlag = oldGitFlag
-		ResetFlag = oldResetFlag
-		LogLevel = oldLogLevel
-	}()
-
-	args := []string{"*.go", "return x", "file1.go", "file2.go"}
-
-	// Execute
-	commands, err := LoadCommandFromArgs(args)
-
-	// Assert
-	assert.NoError(t, err)
-	assert.Len(t, commands, 1)
-	assert.Equal(t, "*.go", commands[0].Regex)
-	assert.Equal(t, "return x", commands[0].Lua)
-	assert.Equal(t, []string{"file1.go", "file2.go"}, commands[0].Files)
-	assert.Equal(t, true, commands[0].Git)
-	assert.Equal(t, false, commands[0].Reset)
-	assert.Equal(t, "info", commands[0].LogLevel)
-}
-
-// Less than 3 arguments returns an error with appropriate message
-func TestLoadCommandFromArgsWithInsufficientArguments(t *testing.T) {
-	// Setup
-	oldGitFlag := GitFlag
-	oldResetFlag := ResetFlag
-	oldLogLevel := LogLevel
-
-	gitValue := false
-	resetValue := false
-	logLevelValue := "info"
-
-	GitFlag = &gitValue
-	ResetFlag = &resetValue
-	LogLevel = &logLevelValue
-
-	defer func() {
-		GitFlag = oldGitFlag
-		ResetFlag = oldResetFlag
-		LogLevel = oldLogLevel
-	}()
-
-	testCases := []struct {
-		name string
-		args []string
-	}{
-		{"empty args", []string{}},
-		{"one arg", []string{"*.go"}},
-		{"two args", []string{"*.go", "return x"}},
-	}
-
-	for _, tc := range testCases {
-		t.Run(tc.name, func(t *testing.T) {
-			// Execute
-			commands, err := LoadCommandFromArgs(tc.args)
-
-			// Assert
-			assert.Error(t, err)
-			assert.Nil(t, commands)
-			assert.Contains(t, err.Error(), "at least 3 arguments are required")
-		})
-	}
-}
-
-// Pattern, Lua, and Files fields are correctly populated from args
-func TestLoadCommandFromArgsPopulatesFieldsCorrectly(t *testing.T) {
-	// Setup
-	oldGitFlag := GitFlag
-	oldResetFlag := ResetFlag
-	oldLogLevel := LogLevel
-
-	gitValue := false
-	resetValue := false
-	logLevelValue := "debug"
-
-	GitFlag = &gitValue
-	ResetFlag = &resetValue
-	LogLevel = &logLevelValue
-
-	defer func() {
-		GitFlag = oldGitFlag
-		ResetFlag = oldResetFlag
-		LogLevel = oldLogLevel
-	}()
-
-	args := []string{"*.txt", "print('Hello')", "file1.txt", "file2.txt"}
-
-	// Execute
-	commands, err := LoadCommandFromArgs(args)
-
-	// Assert
-	assert.NoError(t, err)
-	assert.Len(t, commands, 1)
-	assert.Equal(t, "*.txt", commands[0].Regex)
-	assert.Equal(t, "print('Hello')", commands[0].Lua)
-	assert.Equal(t, []string{"file1.txt", "file2.txt"}, commands[0].Files)
-	assert.Equal(t, false, commands[0].Git)
-	assert.Equal(t, false, commands[0].Reset)
-	assert.Equal(t, "debug", commands[0].LogLevel)
-}
-
-// Git flag is set to true when ResetFlag is true
-func TestLoadCommandFromArgsSetsGitFlagWhenResetFlagIsTrue(t *testing.T) {
-	// Setup
-	oldGitFlag := GitFlag
-	oldResetFlag := ResetFlag
-	oldLogLevel := LogLevel
-
-	gitValue := false
-	resetValue := true
-	logLevelValue := "info"
-
-	GitFlag = &gitValue
-	ResetFlag = &resetValue
-	LogLevel = &logLevelValue
-
-	defer func() {
-		GitFlag = oldGitFlag
-		ResetFlag = oldResetFlag
-		LogLevel = oldLogLevel
-	}()
-
-	args := []string{"*.go", "return x", "file1.go", "file2.go"}
-
-	// Execute
-	commands, err := LoadCommandFromArgs(args)
-
-	// Assert
-	assert.NoError(t, err)
-	assert.Len(t, commands, 1)
-	assert.Equal(t, true, commands[0].Git)
-}
-
 // TODO: Figure out how to mock shit
 // Can't be asked doing that right now...
 // Successfully loads commands from multiple YAML files in the current directory
@@ -803,7 +547,7 @@ func TestLoadCommandsFromCookFilesNoYamlFiles(t *testing.T) {
 	}
 
 	// Execute function
-	commands, err := LoadCommandsFromCookFiles("")
+	commands, _, err := LoadCommandsFromCookFiles("")
 
 	// Assertions
 	if err != nil {
@@ -869,7 +613,7 @@ func TestLoadCommandsFromCookFilesNoYamlFiles(t *testing.T) {
 // 	}
 //
 // 	// Execute function
-// 	commands, err := LoadCommandsFromCookFiles("")
+// 	commands, _, err := LoadCommandsFromCookFiles("")
 //
 // 	// Assertions
 // 	if err != nil {
@@ -953,7 +697,7 @@ func TestLoadCommandsFromCookFilesNoYamlFiles(t *testing.T) {
 // 	}
 //
 // 	// Execute function
-// 	commands, err := LoadCommandsFromCookFiles("")
+// 	commands, _, err := LoadCommandsFromCookFiles("")
 //
 // 	// Assertions
 // 	if err != nil {
@@ -965,6 +709,58 @@ func TestLoadCommandsFromCookFilesNoYamlFiles(t *testing.T) {
 // 	}
 // }
 
+func TestExpandGlobsMemoization(t *testing.T) {
+	tmpDir, err := os.MkdirTemp("", "expand-globs-memo-test")
+	if err != nil {
+		t.Fatalf("Failed to create temp dir: %v", err)
+	}
+	defer os.RemoveAll(tmpDir)
+
+	err = os.WriteFile(filepath.Join(tmpDir, "test1.go"), []byte("test"), 0644)
+	if err != nil {
+		t.Fatalf("Failed to create test file: %v", err)
+	}
+	err = os.WriteFile(filepath.Join(tmpDir, "test2.go"), []byte("test"), 0644)
+	if err != nil {
+		t.Fatalf("Failed to create test file: %v", err)
+	}
+
+	origDir, _ := os.Getwd()
+	os.Chdir(tmpDir)
+	defer os.Chdir(origDir)
+
+	cwd, _ := os.Getwd()
+	resolvedCwd := ResolvePath(cwd)
+	pattern1 := resolvedCwd + "/*.go"
+	patterns := map[string]struct{}{pattern1: {}}
+
+	globMemoTable = make(map[string][]string)
+
+	files1, err := ExpandGlobs(patterns)
+	if err != nil {
+		t.Fatalf("ExpandGlobs failed: %v", err)
+	}
+	if len(files1) != 2 {
+		t.Fatalf("Expected 2 files, got %d", len(files1))
+	}
+
+	if len(globMemoTable) != 1 {
+		t.Fatalf("Expected 1 entry in memo table, got %d", len(globMemoTable))
+	}
+
+	files2, err := ExpandGlobs(patterns)
+	if err != nil {
+		t.Fatalf("ExpandGlobs failed: %v", err)
+	}
+	if len(files2) != 2 {
+		t.Fatalf("Expected 2 files, got %d", len(files2))
+	}
+
+	if len(globMemoTable) != 1 {
+		t.Fatalf("Expected memo table to still have 1 entry, got %d", len(globMemoTable))
+	}
+}
+
 // LoadCommandsFromCookFile returns an error for a malformed YAML file
 // func TestLoadCommandsFromCookFilesMalformedYAML(t *testing.T) {
 // 	// Setup test directory with mock YAML files
@@ -1060,7 +856,7 @@ func TestLoadCommandsFromCookFilesNoYamlFiles(t *testing.T) {
 // 	}
 //
 // 	// Execute function
-// 	commands, err := LoadCommandsFromCookFiles("")
+// 	commands, _, err := LoadCommandsFromCookFiles("")
 //
 // 	// Assertions
 // 	if err == nil {
@@ -1127,7 +923,7 @@ func TestLoadCommandsFromCookFilesNoYamlFiles(t *testing.T) {
 // 	}
 //
 // 	// Execute function
-// 	commands, err := LoadCommandsFromCookFiles("")
+// 	commands, _, err := LoadCommandsFromCookFiles("")
 //
 // 	// Assertions
 // 	if err != nil {
@@ -1197,7 +993,7 @@ func TestLoadCommandsFromCookFilesNoYamlFiles(t *testing.T) {
 // 	}
 //
 // 	// Execute function
-// 	commands, err := LoadCommandsFromCookFiles("")
+// 	commands, _, err := LoadCommandsFromCookFiles("")
 //
 // 	// Assertions
 // 	if err != nil {
@@ -1255,7 +1051,7 @@ func TestLoadCommandsFromCookFilesNoYamlFiles(t *testing.T) {
 // 	}
 //
 // 	// Execute function
-// 	commands, err := LoadCommandsFromCookFiles("")
+// 	commands, _, err := LoadCommandsFromCookFiles("")
 //
 // 	// Assertions
 // 	if err != nil {

utils/modifycommand_yaml_convert_test.go

@@ -0,0 +1,93 @@
+package utils
+
+import (
+	"os"
+	"path/filepath"
+	"testing"
+
+	"github.com/stretchr/testify/assert"
+)
+
+// TestConvertYAMLToTOMLReadError tests error handling when YAML file can't be read
+func TestConvertYAMLToTOMLReadError(t *testing.T) {
+	tmpDir, err := os.MkdirTemp("", "convert-read-error-*")
+	assert.NoError(t, err)
+	defer os.RemoveAll(tmpDir)
+
+	// Create YAML file with no read permissions (on Unix) or delete it after creation
+	yamlFile := filepath.Join(tmpDir, "test.yml")
+	err = os.WriteFile(yamlFile, []byte("commands:\n  - name: test\n"), 0000)
+	assert.NoError(t, err)
+
+	origDir, _ := os.Getwd()
+	defer os.Chdir(origDir)
+	os.Chdir(tmpDir)
+
+	// This should fail to read but not crash
+	err = ConvertYAMLToTOML("test.yml")
+	// Function continues on error, doesn't return error
+	assert.NoError(t, err)
+
+	// Fix permissions for cleanup
+	os.Chmod(yamlFile, 0644)
+}
+
+// TestConvertYAMLToTOMLParseError tests error handling when YAML is invalid
+func TestConvertYAMLToTOMLParseError(t *testing.T) {
+	tmpDir, err := os.MkdirTemp("", "convert-parse-error-*")
+	assert.NoError(t, err)
+	defer os.RemoveAll(tmpDir)
+
+	// Create invalid YAML
+	yamlFile := filepath.Join(tmpDir, "invalid.yml")
+	err = os.WriteFile(yamlFile, []byte("commands:\n  - [this is not valid yaml}}"), 0644)
+	assert.NoError(t, err)
+
+	origDir, _ := os.Getwd()
+	defer os.Chdir(origDir)
+	os.Chdir(tmpDir)
+
+	// This should fail to parse but not crash
+	err = ConvertYAMLToTOML("invalid.yml")
+	assert.NoError(t, err)
+
+	// TOML file should not exist
+	_, statErr := os.Stat(filepath.Join(tmpDir, "invalid.toml"))
+	assert.True(t, os.IsNotExist(statErr))
+}
+
+// TestConvertYAMLToTOMLWriteError tests error handling when TOML file can't be written
+func TestConvertYAMLToTOMLWriteError(t *testing.T) {
+	if os.Getenv("CI") != "" {
+		t.Skip("Skipping write permission test in CI")
+	}
+
+	tmpDir, err := os.MkdirTemp("", "convert-write-error-*")
+	assert.NoError(t, err)
+	defer os.RemoveAll(tmpDir)
+
+	// Create valid YAML
+	yamlFile := filepath.Join(tmpDir, "test.yml")
+	err = os.WriteFile(yamlFile, []byte("commands:\n  - name: test\n    regex: test\n    lua: v1\n    files: [test.txt]\n"), 0644)
+	assert.NoError(t, err)
+
+	// Create output directory with no write permissions
+	outputDir := filepath.Join(tmpDir, "readonly")
+	err = os.Mkdir(outputDir, 0555)
+	assert.NoError(t, err)
+	defer os.Chmod(outputDir, 0755) // Fix for cleanup
+
+	origDir, _ := os.Getwd()
+	defer os.Chdir(origDir)
+	os.Chdir(tmpDir)
+
+	// Move YAML into readonly dir
+	newYamlFile := filepath.Join(outputDir, "test.yml")
+	os.Rename(yamlFile, newYamlFile)
+
+	os.Chdir(outputDir)
+
+	// This should fail to write but not crash
+	err = ConvertYAMLToTOML("test.yml")
+	assert.NoError(t, err)
+}

utils/path.go

@@ -0,0 +1,79 @@
+package utils
+
+import (
+	"os"
+	"path/filepath"
+	"strings"
+
+	logger "git.site.quack-lab.dev/dave/cylogger"
+)
+
+// pathLogger is a scoped logger for the utils/path package.
+var pathLogger = logger.Default.WithPrefix("utils/path")
+
+// ResolvePath resolves a path to an absolute path, handling ~ expansion and cleaning
+func ResolvePath(path string) string {
+	resolvePathLogger := pathLogger.WithPrefix("ResolvePath").WithField("inputPath", path)
+	resolvePathLogger.Trace("Resolving path: %q", path)
+
+	// Handle empty path
+	if path == "" {
+		resolvePathLogger.Trace("Empty path, returning empty string")
+		return ""
+	}
+
+	// Check if path is absolute
+	if filepath.IsAbs(path) {
+		resolvePathLogger.Trace("Path is already absolute: %q", path)
+		cleaned := filepath.ToSlash(filepath.Clean(path))
+		resolvePathLogger.Trace("Cleaned absolute path: %q", cleaned)
+		return cleaned
+	}
+
+	// Handle ~ expansion
+	if strings.HasPrefix(path, "~") {
+		homeDir, _ := os.UserHomeDir()
+		if strings.HasPrefix(path, "~/") || strings.HasPrefix(path, "~\\") {
+			path = filepath.Join(homeDir, path[2:])
+		} else if path == "~" {
+			path = homeDir
+		} else {
+			// ~something (like ~~), treat first ~ as home expansion, rest as literal
+			path = homeDir + path[1:]
+		}
+		resolvePathLogger.Trace("Expanded ~ to home directory: %q", path)
+	}
+
+	// Make absolute if not already
+	if !filepath.IsAbs(path) {
+		absPath, err := filepath.Abs(path)
+		if err != nil {
+			resolvePathLogger.Error("Failed to get absolute path: %v", err)
+			return filepath.ToSlash(filepath.Clean(path))
+		}
+		resolvePathLogger.Trace("Made path absolute: %q -> %q", path, absPath)
+		path = absPath
+	}
+
+	// Clean the path and normalize to forward slashes for consistency
+	cleaned := filepath.ToSlash(filepath.Clean(path))
+	resolvePathLogger.Trace("Final cleaned path: %q", cleaned)
+	return cleaned
+}
+
+// GetRelativePath returns the relative path from base to target
+func GetRelativePath(base, target string) (string, error) {
+	getRelativePathLogger := pathLogger.WithPrefix("GetRelativePath")
+	getRelativePathLogger.Debug("Getting relative path from %q to %q", base, target)
+
+	relPath, err := filepath.Rel(base, target)
+	if err != nil {
+		getRelativePathLogger.Error("Failed to get relative path: %v", err)
+		return "", err
+	}
+
+	// Use forward slashes for consistency
+	relPath = filepath.ToSlash(relPath)
+	getRelativePathLogger.Debug("Relative path: %q", relPath)
+	return relPath, nil
+}

utils/path_test.go

@@ -0,0 +1,386 @@
+package utils
+
+import (
+	"os"
+	"path/filepath"
+	"runtime"
+	"strings"
+	"testing"
+
+	"github.com/stretchr/testify/assert"
+)
+
+func TestResolvePath(t *testing.T) {
+	// Save original working directory
+	origDir, _ := os.Getwd()
+	defer os.Chdir(origDir)
+
+	// Create a temporary directory for testing
+	tmpDir, err := os.MkdirTemp("", "path_test")
+	assert.NoError(t, err)
+	defer os.RemoveAll(tmpDir)
+
+	tests := []struct {
+		name     string
+		input    string
+		expected string
+		setup    func() // Optional setup function
+	}{
+		{
+			name:     "Empty path",
+			input:    "",
+			expected: "",
+		},
+		{
+			name:     "Already absolute path",
+			input:    func() string {
+				if runtime.GOOS == "windows" {
+					return "C:/absolute/path/file.txt"
+				}
+				return "/absolute/path/file.txt"
+			}(),
+			expected: func() string {
+				if runtime.GOOS == "windows" {
+					return "C:/absolute/path/file.txt"
+				}
+				return "/absolute/path/file.txt"
+			}(),
+		},
+		{
+			name:     "Relative path",
+			input:    "relative/file.txt",
+			expected: func() string {
+				abs, _ := filepath.Abs("relative/file.txt")
+				return strings.ReplaceAll(abs, "\\", "/")
+			}(),
+		},
+		{
+			name:     "Tilde expansion - home only",
+			input:    "~",
+			expected: func() string {
+				home := os.Getenv("HOME")
+				if home == "" && runtime.GOOS == "windows" {
+					home = os.Getenv("USERPROFILE")
+				}
+				return strings.ReplaceAll(filepath.Clean(home), "\\", "/")
+			}(),
+		},
+		{
+			name:     "Tilde expansion - with subpath",
+			input:    "~/Documents/file.txt",
+			expected: func() string {
+				home := os.Getenv("HOME")
+				if home == "" && runtime.GOOS == "windows" {
+					home = os.Getenv("USERPROFILE")
+				}
+				expected := filepath.Join(home, "Documents", "file.txt")
+				return strings.ReplaceAll(filepath.Clean(expected), "\\", "/")
+			}(),
+		},
+		{
+			name:     "Path normalization - double slashes",
+			input:    "path//to//file.txt",
+			expected: func() string {
+				abs, _ := filepath.Abs("path/to/file.txt")
+				return strings.ReplaceAll(abs, "\\", "/")
+			}(),
+		},
+		{
+			name:     "Path normalization - . and ..",
+			input:    "path/./to/../file.txt",
+			expected: func() string {
+				abs, _ := filepath.Abs("path/file.txt")
+				return strings.ReplaceAll(abs, "\\", "/")
+			}(),
+		},
+		{
+			name:     "Windows backslash normalization",
+			input:    "path\\to\\file.txt",
+			expected: func() string {
+				abs, _ := filepath.Abs("path/to/file.txt")
+				return strings.ReplaceAll(abs, "\\", "/")
+			}(),
+		},
+		{
+			name:     "Mixed separators with tilde",
+			input:    "~/Documents\\file.txt",
+			expected: func() string {
+				home := os.Getenv("HOME")
+				if home == "" && runtime.GOOS == "windows" {
+					home = os.Getenv("USERPROFILE")
+				}
+				expected := filepath.Join(home, "Documents", "file.txt")
+				return strings.ReplaceAll(filepath.Clean(expected), "\\", "/")
+			}(),
+		},
+		{
+			name:     "Relative path from current directory",
+			input:    "./file.txt",
+			expected: func() string {
+				abs, _ := filepath.Abs("file.txt")
+				return strings.ReplaceAll(abs, "\\", "/")
+			}(),
+		},
+	}
+
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			if tt.setup != nil {
+				tt.setup()
+			}
+
+			result := ResolvePath(tt.input)
+			assert.Equal(t, tt.expected, result, "ResolvePath(%q) = %q, want %q", tt.input, result, tt.expected)
+		})
+	}
+}
+
+func TestResolvePathWithWorkingDirectoryChange(t *testing.T) {
+	// Save original working directory
+	origDir, _ := os.Getwd()
+	defer os.Chdir(origDir)
+
+	// Create temporary directories
+	tmpDir, err := os.MkdirTemp("", "path_test")
+	assert.NoError(t, err)
+	defer os.RemoveAll(tmpDir)
+
+	subDir := filepath.Join(tmpDir, "subdir")
+	err = os.MkdirAll(subDir, 0755)
+	assert.NoError(t, err)
+
+	// Change to subdirectory
+	err = os.Chdir(subDir)
+	assert.NoError(t, err)
+
+	// Test relative path resolution from new working directory
+	result := ResolvePath("../test.txt")
+	expected := filepath.Join(tmpDir, "test.txt")
+	expected = strings.ReplaceAll(filepath.Clean(expected), "\\", "/")
+
+	assert.Equal(t, expected, result)
+}
+
+func TestResolvePathComplexTilde(t *testing.T) {
+	// Test complex tilde patterns
+	home := os.Getenv("HOME")
+	if home == "" && runtime.GOOS == "windows" {
+		home = os.Getenv("USERPROFILE")
+	}
+
+	if home == "" {
+		t.Skip("Cannot determine home directory for tilde expansion tests")
+	}
+
+	tests := []struct {
+		input    string
+		expected string
+	}{
+		{
+			input:    "~",
+			expected: strings.ReplaceAll(filepath.Clean(home), "\\", "/"),
+		},
+		{
+			input:    "~/",
+			expected: strings.ReplaceAll(filepath.Clean(home), "\\", "/"),
+		},
+		{
+			input: "~~",
+			expected: func() string {
+				// ~~ should be treated as ~ followed by ~ (tilde expansion)
+				home := os.Getenv("HOME")
+				if home == "" && runtime.GOOS == "windows" {
+					home = os.Getenv("USERPROFILE")
+				}
+				if home != "" {
+					// First ~ gets expanded, second ~ remains
+					return strings.ReplaceAll(filepath.Clean(home+"~"), "\\", "/")
+				}
+				abs, _ := filepath.Abs("~~")
+				return strings.ReplaceAll(abs, "\\", "/")
+			}(),
+		},
+		{
+			input: func() string {
+				if runtime.GOOS == "windows" {
+					return "C:/not/tilde/path"
+				}
+				return "/not/tilde/path"
+			}(),
+			expected: func() string {
+				if runtime.GOOS == "windows" {
+					return "C:/not/tilde/path"
+				}
+				return "/not/tilde/path"
+			}(),
+		},
+	}
+
+	for _, tt := range tests {
+		t.Run("Complex tilde: "+tt.input, func(t *testing.T) {
+			result := ResolvePath(tt.input)
+			assert.Equal(t, tt.expected, result)
+		})
+	}
+}
+
+
+func TestGetRelativePath(t *testing.T) {
+	// Create temporary directories for testing
+	tmpDir, err := os.MkdirTemp("", "relative_path_test")
+	assert.NoError(t, err)
+	defer os.RemoveAll(tmpDir)
+
+	baseDir := filepath.Join(tmpDir, "base")
+	targetDir := filepath.Join(tmpDir, "target")
+	subDir := filepath.Join(targetDir, "subdir")
+
+	err = os.MkdirAll(baseDir, 0755)
+	assert.NoError(t, err)
+	err = os.MkdirAll(subDir, 0755)
+	assert.NoError(t, err)
+
+	tests := []struct {
+		name     string
+		base     string
+		target   string
+		expected string
+		wantErr  bool
+	}{
+		{
+			name:     "Target is subdirectory of base",
+			base:     baseDir,
+			target:   filepath.Join(baseDir, "subdir"),
+			expected: "subdir",
+			wantErr:  false,
+		},
+		{
+			name:     "Target is parent of base",
+			base:     filepath.Join(baseDir, "subdir"),
+			target:   baseDir,
+			expected: "..",
+			wantErr:  false,
+		},
+		{
+			name:     "Target is sibling directory",
+			base:     baseDir,
+			target:   targetDir,
+			expected: "../target",
+			wantErr:  false,
+		},
+		{
+			name:     "Same directory",
+			base:     baseDir,
+			target:   baseDir,
+			expected: ".",
+			wantErr:  false,
+		},
+		{
+			name:     "With tilde expansion",
+			base:     baseDir,
+			target:   filepath.Join(baseDir, "file.txt"),
+			expected: "file.txt",
+			wantErr:  false,
+		},
+	}
+
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			result, err := GetRelativePath(tt.base, tt.target)
+			if tt.wantErr {
+				assert.Error(t, err)
+			} else {
+				assert.NoError(t, err)
+				assert.Equal(t, tt.expected, result)
+			}
+		})
+	}
+}
+
+func TestResolvePathRegression(t *testing.T) {
+	// This test specifically addresses the original bug:
+	// "~ is NOT BEING FUCKING RESOLVED"
+
+	home := os.Getenv("HOME")
+	if home == "" && runtime.GOOS == "windows" {
+		home = os.Getenv("USERPROFILE")
+	}
+
+	if home == "" {
+		t.Skip("Cannot determine home directory for regression test")
+	}
+
+	// Test the exact pattern from the bug report
+	testPath := "~/Seafile/activitywatch/sync.yml"
+	result := ResolvePath(testPath)
+	expected := filepath.Join(home, "Seafile", "activitywatch", "sync.yml")
+	expected = strings.ReplaceAll(filepath.Clean(expected), "\\", "/")
+
+	assert.Equal(t, expected, result, "Tilde expansion bug not fixed!")
+	assert.NotContains(t, result, "~", "Tilde still present in resolved path!")
+	// Convert both to forward slashes for comparison
+	homeForwardSlash := strings.ReplaceAll(home, "\\", "/")
+	assert.Contains(t, result, homeForwardSlash, "Home directory not found in resolved path!")
+}
+
+func TestResolvePathEdgeCases(t *testing.T) {
+	// Save original working directory
+	origDir, _ := os.Getwd()
+	defer os.Chdir(origDir)
+
+	tests := []struct {
+		name        string
+		input       string
+		setup       func()
+		shouldPanic bool
+	}{
+		{
+			name:  "Just dot",
+			input: ".",
+		},
+		{
+			name:  "Just double dot",
+			input: "..",
+		},
+		{
+			name:  "Triple dot",
+			input: "...",
+		},
+		{
+			name:  "Multiple leading dots",
+			input: "./.././../file.txt",
+		},
+		{
+			name:  "Path with spaces",
+			input: "path with spaces/file.txt",
+		},
+		{
+			name:  "Very long relative path",
+			input: strings.Repeat("../", 10) + "file.txt",
+		},
+	}
+
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			if tt.setup != nil {
+				tt.setup()
+			}
+
+			if tt.shouldPanic {
+				assert.Panics(t, func() {
+					ResolvePath(tt.input)
+				})
+			} else {
+				// Should not panic
+				assert.NotPanics(t, func() {
+					ResolvePath(tt.input)
+				})
+				// Result should be a valid absolute path
+				result := ResolvePath(tt.input)
+				if tt.input != "" {
+					assert.True(t, filepath.IsAbs(result) || result == "", "Result should be absolute or empty")
+				}
+			}
+		})
+	}
+}

utils/replacecommand.go

@@ -2,10 +2,14 @@ package utils
 
 import (
 	"fmt"
-	"modify/logger"
 	"sort"
+
+	logger "git.site.quack-lab.dev/dave/cylogger"
 )
 
+// replaceCommandLogger is a scoped logger for the utils/replacecommand package.
+var replaceCommandLogger = logger.Default.WithPrefix("utils/replacecommand")
+
 type ReplaceCommand struct {
 	From int
 	To   int
@@ -13,45 +17,63 @@ type ReplaceCommand struct {
 }
 
 func ExecuteModifications(modifications []ReplaceCommand, fileData string) (string, int) {
+	executeModificationsLogger := replaceCommandLogger.WithPrefix("ExecuteModifications")
+	executeModificationsLogger.Debug("Executing a batch of text modifications")
+	executeModificationsLogger.Trace("Number of modifications: %d, Original file data length: %d", len(modifications), len(fileData))
 	var err error
 
 	sort.Slice(modifications, func(i, j int) bool {
 		return modifications[i].From > modifications[j].From
 	})
-	logger.Trace("Preparing to apply %d replacement commands in reverse order", len(modifications))
+	executeModificationsLogger.Debug("Modifications sorted in reverse order for safe replacement")
+	executeModificationsLogger.Trace("Sorted modifications: %v", modifications)
 
 	executed := 0
-	for _, modification := range modifications {
+	for idx, modification := range modifications {
+		executeModificationsLogger.Debug("Applying modification %d/%d", idx+1, len(modifications))
+		executeModificationsLogger.Trace("Current modification details: From=%d, To=%d, With=%q", modification.From, modification.To, modification.With)
 		fileData, err = modification.Execute(fileData)
 		if err != nil {
-			logger.Error("Failed to execute replacement: %v", err)
+			executeModificationsLogger.Error("Failed to execute replacement for modification %+v: %v", modification, err)
 			continue
 		}
 		executed++
+		executeModificationsLogger.Trace("File data length after modification: %d", len(fileData))
 	}
-	logger.Info("Successfully applied %d text replacements", executed)
+	executeModificationsLogger.Info("Successfully applied %d text replacements", executed)
 	return fileData, executed
 }
 
 func (m *ReplaceCommand) Execute(fileDataStr string) (string, error) {
+	executeLogger := replaceCommandLogger.WithPrefix("Execute").WithField("modification", fmt.Sprintf("From:%d,To:%d,With:%q", m.From, m.To, m.With))
+	executeLogger.Debug("Attempting to execute single replacement")
 	err := m.Validate(len(fileDataStr))
 	if err != nil {
+		executeLogger.Error("Failed to validate modification: %v", err)
 		return fileDataStr, fmt.Errorf("failed to validate modification: %v", err)
 	}
 
-	logger.Trace("Replace pos %d-%d with %q", m.From, m.To, m.With)
-	return fileDataStr[:m.From] + m.With + fileDataStr[m.To:], nil
+	executeLogger.Trace("Applying replacement: fileDataStr[:%d] + %q + fileDataStr[%d:]", m.From, m.With, m.To)
+	result := fileDataStr[:m.From] + m.With + fileDataStr[m.To:]
+	executeLogger.Trace("Replacement executed. Result length: %d", len(result))
+	return result, nil
 }
 
 func (m *ReplaceCommand) Validate(maxsize int) error {
+	validateLogger := replaceCommandLogger.WithPrefix("Validate").WithField("modification", fmt.Sprintf("From:%d,To:%d,With:%q", m.From, m.To, m.With)).WithField("maxSize", maxsize)
+	validateLogger.Debug("Validating replacement command against max size")
 	if m.To < m.From {
+		validateLogger.Error("Validation failed: 'To' (%d) is less than 'From' (%d)", m.To, m.From)
 		return fmt.Errorf("command to is less than from: %v", m)
 	}
 	if m.From > maxsize || m.To > maxsize {
+		validateLogger.Error("Validation failed: 'From' (%d) or 'To' (%d) is greater than max size (%d)", m.From, m.To, maxsize)
 		return fmt.Errorf("command from or to is greater than replacement length: %v", m)
 	}
 	if m.From < 0 || m.To < 0 {
+		validateLogger.Error("Validation failed: 'From' (%d) or 'To' (%d) is less than 0", m.From, m.To)
 		return fmt.Errorf("command from or to is less than 0: %v", m)
 	}
+	validateLogger.Debug("Modification command validated successfully")
 	return nil
 }