Use diffs for tests

Hallucinate more logs

fix(utils/db.go): handle auto migration errors gracefully

fix(utils/modifycommand.go): improve file matching accuracy

fix(processor/regex.go): improve capture group deduplication logic

fix(utils/db.go): add logging for database wrapper initialization

feat(processor/regex.go): preserve input order when deduplicating capture groups

fix(utils/modifycommand.go): add logging for file matching skips

feat(processor/regex.go): add logging for capture group processing

feat(main.go): add trace logging for arguments and parallel workers

fix(main.go): add trace logging for file content

fix(utils/db.go): add logging for database opening

fix(main.go): add trace logging for file processing

fix(utils/modifycommand.go): improve file matching by using absolute paths

feat(modifycommand.go): add trace logging for file matching in AssociateFilesWithCommands

feat(main.go): add per-file association summary for better visibility when debugging

.gitignore

@@ -1,3 +1,4 @@
 *.exe
 .qodo
 *.sqlite
+testfiles

.vscode/launch.json

@@ -98,6 +98,19 @@
 			"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",
+				"cook_processorrecipes.yml",
+			]
 		}
 	]
 }

go.mod

@@ -13,7 +13,6 @@ require (
 
 require (
 	github.com/davecgh/go-spew v1.1.1 // indirect
-	github.com/google/go-cmp v0.6.0 // indirect
 	github.com/hexops/valast v1.5.0 // indirect
 	github.com/jinzhu/inflection v1.0.0 // indirect
 	github.com/jinzhu/now v1.1.5 // indirect
@@ -21,6 +20,8 @@ require (
 	github.com/mattn/go-sqlite3 v1.14.22 // indirect
 	github.com/pmezard/go-difflib v1.0.0 // indirect
 	github.com/rogpeppe/go-internal v1.14.1 // 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
@@ -29,4 +30,8 @@ require (
 	mvdan.cc/gofumpt v0.4.0 // indirect
 )
 
-require gorm.io/driver/sqlite v1.6.0
+require (
+	github.com/google/go-cmp v0.6.0
+	github.com/tidwall/gjson v1.18.0
+	gorm.io/driver/sqlite v1.6.0
+)

go.sum

@@ -36,6 +36,12 @@ github.com/rogpeppe/go-internal v1.14.1 h1:UQB4HGPB6osV0SQTLymcB4TgvyWu6ZyliaW0t
 github.com/rogpeppe/go-internal v1.14.1/go.mod h1:MaRKkUm5W0goXpeCfT7UZI6fk/L7L7so1lCWt35ZSgc=
 github.com/stretchr/testify v1.10.0 h1:Xv5erBjTwe/5IxqUQTdXv5kgmIvbHo3QQyRwhJsOfJA=
 github.com/stretchr/testify v1.10.0/go.mod h1:r2ic/lqez/lEtzL7wO/rwa5dbSLXVDPFyf8C91i36aY=
+github.com/tidwall/gjson v1.18.0 h1:FIDeeyB800efLX89e5a8Y0BNH+LOngJyGrIWxG2FKQY=
+github.com/tidwall/gjson v1.18.0/go.mod h1:/wbyibRr2FHMks5tjHJ5F8dMZh3AcwJEMf5vlfC0lxk=
+github.com/tidwall/match v1.1.1 h1:+Ho715JplO36QYgwN9PGYNhgZvoUSc9X2c80KVTi+GA=
+github.com/tidwall/match v1.1.1/go.mod h1:eRSPERbgtNPcGhD8UCthc6PmLEQXEWd3PRB5JTxsfmM=
+github.com/tidwall/pretty v1.2.0 h1:RWIZEg2iJ8/g6fDDYzMpobmaoGh5OLl4AXtGUGPcqCs=
+github.com/tidwall/pretty v1.2.0/go.mod h1:ITEVvHYasfjBbM0u2Pg8T2nJnzm8xPwvNhhsoaGGjNU=
 github.com/yuin/gopher-lua v1.1.1 h1:kYKnWBjvbNP4XLT3+bPEwAXJx262OhaHDWDVOPjL46M=
 github.com/yuin/gopher-lua v1.1.1/go.mod h1:GBR0iDaNXjAgGg9zfCvksxSRnQx76gclCIb7kdAd1Pw=
 golang.org/x/mod v0.21.0 h1:vvrHzRwRfVKSiLrG+d4FMl/Qi4ukBCE6kZlTUkDYRT0=

main.go

@@ -1,11 +1,13 @@
 package main
 
 import (
+	"errors"
 	"flag"
 	"fmt"
 	"os"
 	"sort"
 	"sync"
+	"sync/atomic"
 	"time"
 
 	"cook/processor"
@@ -16,11 +18,14 @@ import (
 	logger "git.site.quack-lab.dev/dave/cylogger"
 )
 
+// mainLogger is a scoped logger for the main package.
+var mainLogger = logger.Default.WithPrefix("main")
+
 type GlobalStats struct {
-	TotalMatches            int
+	TotalMatches            int64
-	TotalModifications      int
+	TotalModifications      int64
-	ProcessedFiles          int
+	ProcessedFiles          int64
-	FailedFiles             int
+	FailedFiles             int64
 	ModificationsPerCommand sync.Map
 }
 
@@ -39,9 +44,13 @@ func main() {
 		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, "  -json\n")
+		fmt.Fprintf(os.Stderr, "        Enable JSON mode for processing JSON files\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, "    %s \"<value>(\\\\d+)</value>\" \"*1.5\" data.xml\n", os.Args[0])
+		fmt.Fprintf(os.Stderr, "  JSON mode:\n")
+		fmt.Fprintf(os.Stderr, "    %s -json data.json\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")
@@ -49,95 +58,147 @@ func main() {
 		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")
+		fmt.Fprintf(os.Stderr, "\nLua Functions Available:\n")
+		fmt.Fprintf(os.Stderr, "%s\n", processor.GetLuaFunctionsHelp())
 	}
 	// TODO: Fix bed shitting when doing *.yml in barotrauma directory
 	flag.Parse()
 	args := flag.Args()
 
 	logger.InitFlag()
-	logger.Info("Initializing with log level: %s", logger.GetLevel().String())
+	mainLogger.Info("Initializing with log level: %s", logger.GetLevel().String())
+	mainLogger.Trace("Full argv: %v", os.Args)
 
 	if flag.NArg() == 0 {
 		flag.Usage()
 		return
 	}
 
+	mainLogger.Debug("Getting database connection")
 	db, err := utils.GetDB()
 	if err != nil {
-		logger.Error("Failed to get database: %v", err)
+		mainLogger.Error("Failed to get database: %v", err)
 		return
 	}
+	mainLogger.Debug("Database connection established")
 
 	workdone, err := HandleSpecialArgs(args, err, db)
 	if err != nil {
-		logger.Error("Failed to handle special args: %v", err)
+		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
+	mainLogger.Debug("Loading commands from arguments")
+	mainLogger.Trace("Arguments: %v", args)
 	commands, err := utils.LoadCommands(args)
 	if err != nil || len(commands) == 0 {
-		logger.Error("Failed to load commands: %v", err)
+		mainLogger.Error("Failed to load commands: %v", err)
 		flag.Usage()
 		return
 	}
+	// Collect global modifiers from special entries and filter them out
+	vars := map[string]interface{}{}
+	filtered := make([]utils.ModifyCommand, 0, len(commands))
+	for _, c := range commands {
+		if len(c.Modifiers) > 0 && c.Name == "" && c.Regex == "" && len(c.Regexes) == 0 && c.Lua == "" && len(c.Files) == 0 {
+			for k, v := range c.Modifiers {
+				vars[k] = v
+			}
+			continue
+		}
+		filtered = append(filtered, c)
+	}
+	if len(vars) > 0 {
+		mainLogger.Info("Loaded %d global modifiers", len(vars))
+		processor.SetVariables(vars)
+	}
+	commands = filtered
+	mainLogger.Info("Loaded %d commands", len(commands))
 
 	if *utils.Filter != "" {
-		logger.Info("Filtering commands by name: %s", *utils.Filter)
+		mainLogger.Info("Filtering commands by name: %s", *utils.Filter)
 		commands = utils.FilterCommands(commands, *utils.Filter)
-		logger.Info("Filtered %d commands", len(commands))
+		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 {
-		logger.Trace("Command: %s", command.Name)
+		mainLogger.Trace("Command: %s", command.Name)
-		logger.Trace("Regex: %s", command.Regex)
+		if len(command.Regexes) > 0 {
-		logger.Trace("Files: %v", command.Files)
+			mainLogger.Trace("Regexes: %v", command.Regexes)
-		logger.Trace("Lua: %s", command.Lua)
+		} else {
-		logger.Trace("Reset: %t", command.Reset)
+			mainLogger.Trace("Regex: %s", command.Regex)
-		logger.Trace("Isolate: %t", command.Isolate)
+		}
-		logger.Trace("LogLevel: %s", command.LogLevel)
+		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))
+	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 {
-		logger.Error("Failed to reset files where necessary: %v", err)
+		mainLogger.Error("Failed to reset files where necessary: %v", err)
 		return
 	}
+	mainLogger.Debug("Files reset where necessary")
 
 	// Then for each file run all commands associated with the file
 	workers := make(chan struct{}, *utils.ParallelFiles)
 	wg := sync.WaitGroup{}
+	mainLogger.Debug("Starting file processing with %d parallel workers", *utils.ParallelFiles)
 
 	// Add performance tracking
 	startTime := time.Now()
-	var fileMutex sync.Mutex
 
 	// Create a map to store loggers for each command
 	commandLoggers := make(map[string]*logger.Logger)
@@ -157,10 +218,10 @@ func main() {
 		cmdLogLevel := logger.ParseLevel(command.LogLevel)
 
 		// Create a logger with the command name as a field
-		commandLoggers[command.Name] = logger.WithField("command", cmdName)
+		commandLoggers[command.Name] = logger.Default.WithField("command", cmdName)
 		commandLoggers[command.Name].SetLevel(cmdLogLevel)
 
-		logger.Debug("Created logger for command %q with log level %s", cmdName, cmdLogLevel.String())
+		mainLogger.Debug("Created logger for command %q with log level %s", cmdName, cmdLogLevel.String())
 	}
 
 	for file, association := range associations {
@@ -172,51 +233,72 @@ func main() {
 			// Track per-file processing time
 			fileStartTime := time.Now()
 
-			logger.Debug("Reading file %q", file)
+			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
 			}
 			fileDataStr := string(fileData)
+			mainLogger.Trace("File %q content: %s", file, utils.LimitString(fileDataStr, 500))
 
-			logger.Debug("Saving file %q to database", file)
+			isChanged := false
-			err = db.SaveFile(file, fileData)
+			mainLogger.Debug("Running isolate commands for file %q", file)
-			if err != nil {
+			fileDataStr, err = RunIsolateCommands(association, file, fileDataStr)
-				logger.Error("Failed to save file %q to database: %v", file, err)
+			if err != nil && err != NothingToDo {
+				mainLogger.Error("Failed to run isolate commands for file %q: %v", file, err)
+				atomic.AddInt64(&stats.FailedFiles, 1)
 				return
 			}
-
+			if err != NothingToDo {
-			logger.Debug("Running isolate commands for file %q", file)
+				isChanged = true
-			fileDataStr, err = RunIsolateCommands(association, file, fileDataStr, &fileMutex)
-			if err != nil {
-				logger.Error("Failed to run isolate commands for file %q: %v", file, err)
-				return
 			}
 
-			logger.Debug("Running other commands for file %q", file)
+			mainLogger.Debug("Running other commands for file %q", file)
-			fileDataStr, err = RunOtherCommands(file, fileDataStr, association, &fileMutex, commandLoggers)
+			fileDataStr, err = RunOtherCommands(file, fileDataStr, association, commandLoggers)
-			if err != nil {
+			if err != nil && err != NothingToDo {
-				logger.Error("Failed to run other commands for file %q: %v", file, err)
+				mainLogger.Error("Failed to run other commands for file %q: %v", file, err)
+				atomic.AddInt64(&stats.FailedFiles, 1)
 				return
 			}
+			if err != NothingToDo {
+				isChanged = true
+			}
 
-			logger.Debug("Writing file %q", file)
+			if isChanged {
+				mainLogger.Debug("Saving file %q to database", file)
+				err = db.SaveFile(file, fileData)
+				if err != nil {
+					mainLogger.Error("Failed to save file %q to database: %v", file, err)
+					atomic.AddInt64(&stats.FailedFiles, 1)
+					return
+				}
+				mainLogger.Debug("File %q saved to database", 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)
+	mainLogger.Info("Processing completed in %v", processingTime)
-	if stats.ProcessedFiles > 0 {
+	processedFiles := atomic.LoadInt64(&stats.ProcessedFiles)
-		logger.Info("Average time per file: %v", processingTime/time.Duration(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?
@@ -226,44 +308,46 @@ func main() {
 	// TODO: What to do with git? Figure it out ....
 
 	// if *gitFlag {
-	// 	logger.Info("Git integration enabled, setting up git repository")
+	// 	mainLogger.Info("Git integration enabled, setting up git repository")
 	// 	err := setupGit()
 	// 	if err != nil {
-	// 		logger.Error("Failed to setup git: %v", err)
+	// 		mainLogger.Error("Failed to setup git: %v", err)
 	// 		fmt.Fprintf(os.Stderr, "Error setting up git: %v\n", err)
 	// 		return
 	// 	}
 	// }
 
-	// logger.Debug("Expanding file patterns")
+	// mainLogger.Debug("Expanding file patterns")
 	// files, err := expandFilePatterns(filePatterns)
 	// if err != nil {
-	// 	logger.Error("Failed to expand file patterns: %v", err)
+	// 	mainLogger.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")
+	// 	mainLogger.Info("Cleaning up git files before processing")
 	// 	err := cleanupGitFiles(files)
 	// 	if err != nil {
-	// 		logger.Error("Failed to cleanup git files: %v", err)
+	// 		mainLogger.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")
+	// 	mainLogger.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 {
+	totalModifications := atomic.LoadInt64(&stats.TotalModifications)
-		logger.Warning("No modifications were made in any files")
+	if totalModifications == 0 {
+		mainLogger.Warning("No modifications were made in any files")
 	} else {
-		logger.Info("Operation complete! Modified %d values in %d/%d files",
+		failedFiles := atomic.LoadInt64(&stats.FailedFiles)
-			stats.TotalModifications, stats.ProcessedFiles, stats.ProcessedFiles+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))
@@ -274,148 +358,346 @@ func main() {
 		for _, command := range sortedCommands {
 			count, _ := stats.ModificationsPerCommand.Load(command)
 			if count.(int) > 0 {
-				logger.Info("\tCommand %q made %d modifications", command, count)
+				mainLogger.Info("\tCommand %q made %d modifications", command, count)
 			} else {
-				logger.Warning("\tCommand %q made no modifications", command)
+				mainLogger.Warning("\tCommand %q made no modifications", command)
 			}
 		}
 	}
 }
 
 func HandleSpecialArgs(args []string, err error, db utils.DB) (bool, error) {
+	handleSpecialArgsLogger := logger.Default.WithPrefix("HandleSpecialArgs")
+	handleSpecialArgsLogger.Debug("Handling special arguments: %v", args)
 	switch args[0] {
 	case "reset":
+		handleSpecialArgsLogger.Info("Resetting all files")
 		err = utils.ResetAllFiles(db)
 		if err != nil {
-			logger.Error("Failed to reset all files: %v", err)
+			handleSpecialArgsLogger.Error("Failed to reset all files: %v", err)
 			return true, err
 		}
-		logger.Info("All files reset")
+		handleSpecialArgsLogger.Info("All files reset")
 		return true, nil
 	case "dump":
+		handleSpecialArgsLogger.Info("Dumping all files from database")
 		err = db.RemoveAllFiles()
 		if err != nil {
-			logger.Error("Failed to remove all files from database: %v", err)
+			handleSpecialArgsLogger.Error("Failed to remove all files from database: %v", err)
 			return true, err
 		}
-		logger.Info("All files removed from database")
+		handleSpecialArgsLogger.Info("All files removed from database")
 		return true, nil
 	}
+	handleSpecialArgsLogger.Debug("No special arguments handled, returning false")
 	return false, nil
 }
 
 func CreateExampleConfig() {
+	createExampleConfigLogger := logger.Default.WithPrefix("CreateExampleConfig")
+	createExampleConfigLogger.Debug("Creating example configuration file")
 	commands := []utils.ModifyCommand{
+		// Global modifiers only entry (no name/regex/lua/files)
 		{
-			Name:     "DoubleNumericValues",
+			Modifiers: map[string]interface{}{
-			Regex:    "<value>(\\d+)</value>",
+				"foobar":   4,
-			Lua:      "v1 * 2",
+				"multiply": 1.5,
-			Files:    []string{"data/*.xml"},
+				"prefix":   "NEW_",
-			LogLevel: "INFO",
+				"enabled":  true,
+			},
 		},
+		// Multi-regex example using $variable in Lua
 		{
-			Name:     "UpdatePrices",
+			Name:    "RFToolsMultiply",
-			Regex:    "price=\"(\\d+)\"",
+			Regexes: []string{"generatePerTick = !num", "ticksPer\\w+ = !num", "generatorRFPerTick = !num"},
-			Lua:      "if num(v1) < 100 then return v1 * 1.5 else return v1 end",
+			Lua:     "* $foobar",
-			Files:    []string{"items/*.xml", "shop/*.xml"},
+			Files:   []string{"polymc/instances/**/rftools*.toml", `polymc\\instances\\**\\rftools*.toml`},
+			Reset:   true,
+			// LogLevel defaults to INFO
+		},
+		// Named capture groups with arithmetic and string ops
+		{
+			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: []string{"data/**/*.txt"},
+			// INFO log level
+		},
+		// Full replacement via Lua 'replacement' variable
+		{
+			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: []string{"config/*.ini", "config/*.cfg"},
+		},
+		// Multiline regex example (DOTALL is auto-enabled). Captures numeric in nested XML.
+		{
+			Name:  "XMLNestedValueMultiply",
+			Regex: `<item>\s*\s*<name>!any<\/name>\s*\s*<value>(!num)<\/value>\s*\s*<\/item>`,
+			Lua:   `* $multiply`,
+			Files: []string{"data/**/*.xml"},
+			// Demonstrates multiline regex in YAML
+		},
+		// Multiline regexES array, with different patterns handled by same Lua
+		{
+			Name: "MultiLinePatterns",
+			Regexes: []string{
+				`<entry>\s*\n\s*<id>(?P<id>!num)</id>\s*\n\s*<score>(?P<score>!num)</score>\s*\n\s*</entry>`,
+				`\[block\]\nkey=(?P<key>[A-Za-z_]+)\nvalue=(?P<val>!num)`,
+			},
+			Lua:      `if is_number(score) then score = score * 2 end; if is_number(val) then val = val * 3 end; return true`,
+			Files:    []string{"examples/**/*.*"},
 			LogLevel: "DEBUG",
 		},
+		// Use equals operator shorthand and boolean variable
 		{
-			Name:     "IsolatedTagUpdate",
+			Name:  "EnableFlags",
-			Regex:    "<tag>(.*?)</tag>",
+			Regex: `enabled\s*=\s*(true|false)`,
-			Lua:      "string.upper(s1)",
+			Lua:   `= $enabled`,
-			Files:    []string{"config.xml"},
+			Files: []string{"**/*.toml"},
+		},
+		// Demonstrate NoDedup to allow overlapping replacements
+		{
+			Name:    "OverlappingGroups",
+			Regex:   `(?P<a>!num)(?P<b>!num)`,
+			Lua:     `a = num(a) + 1; b = num(b) + 1; return true`,
+			Files:   []string{"overlap/**/*.txt"},
+			NoDedup: true,
+		},
+		// Isolate command example operating on entire matched block
+		{
+			Name:     "IsolateUppercaseBlock",
+			Regex:    `BEGIN\n(?P<block>!any)\nEND`,
+			Lua:      `block = upper(block); return true`,
+			Files:    []string{"logs/**/*.log"},
 			Isolate:  true,
-			NoDedup:  true,
 			LogLevel: "TRACE",
 		},
+		// Using !rep placeholder and arrays of files
+		{
+			Name:  "RepeatPlaceholderExample",
+			Regex: `name: (.*) !rep(, .* , 2)`,
+			Lua:   `-- no-op, just demonstrate placeholder; return false`,
+			Files: []string{"lists/**/*.yml", "lists/**/*.yaml"},
+		},
+		// Using string variable in Lua expression
+		{
+			Name:  "PrefixKeys",
+			Regex: `(?P<key>[A-Za-z0-9_]+)\s*=`,
+			Lua:   `key = $prefix .. key; return true`,
+			Files: []string{"**/*.properties"},
+		},
+		// JSON mode examples
+		{
+			Name:  "JSONArrayMultiply",
+			JSON:  true,
+			Lua:   `for i, item in ipairs(data.items) do data.items[i].value = item.value * 2 end; return true`,
+			Files: []string{"data/**/*.json"},
+		},
+		{
+			Name:  "JSONObjectUpdate",
+			JSON:  true,
+			Lua:   `data.version = "2.0.0"; data.enabled = true; return true`,
+			Files: []string{"config/**/*.json"},
+		},
+		{
+			Name:  "JSONNestedModify",
+			JSON:  true,
+			Lua:   `if data.settings and data.settings.performance then data.settings.performance.multiplier = data.settings.performance.multiplier * 1.5 end; return true`,
+			Files: []string{"settings/**/*.json"},
+		},
 	}
 
 	data, err := yaml.Marshal(commands)
 	if err != nil {
-		logger.Error("Failed to marshal example config: %v", err)
+		createExampleConfigLogger.Error("Failed to marshal example config: %v", err)
 		return
 	}
 
+	createExampleConfigLogger.Debug("Writing example_cook.yml")
 	err = os.WriteFile("example_cook.yml", data, 0644)
 	if err != nil {
-		logger.Error("Failed to write example_cook.yml: %v", err)
+		createExampleConfigLogger.Error("Failed to write example_cook.yml: %v", err)
 		return
 	}
 
-	logger.Info("Wrote example_cook.yml")
+	createExampleConfigLogger.Info("Wrote example_cook.yml")
 }
 
-func RunOtherCommands(file string, fileDataStr string, association utils.FileCommandAssociation, fileMutex *sync.Mutex, commandLoggers map[string]*logger.Logger) (string, error) {
+var NothingToDo = errors.New("nothing to do")
-	// Aggregate all the modifications and execute them
+
-	modifications := []utils.ReplaceCommand{}
+func RunOtherCommands(file string, fileDataStr string, association utils.FileCommandAssociation, commandLoggers map[string]*logger.Logger) (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 {
-		// Use command-specific logger if available, otherwise fall back to default logger
+		if command.JSON || *utils.JSON {
+			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.Info("Processing file %q with command %q", file, command.Regex)
+		cmdLogger.Debug("Processing file with JSON mode for command %q", command.Name)
-		newModifications, err := processor.ProcessRegex(fileDataStr, command, file)
+		newModifications, err := processor.ProcessJSON(fileDataStr, command, file)
 		if err != nil {
-			logger.Error("Failed to process file %q with command %q: %v", file, command.Regex, err)
+			runOtherCommandsLogger.Error("Failed to process file with JSON command %q: %v", command.Name, err)
 			continue
 		}
-		modifications = append(modifications, newModifications...)
+
-		// It is not guranteed that all the commands will be executed...
+		// Apply JSON modifications immediately
-		// TODO: Make this better
+		if len(newModifications) > 0 {
-		// We'd have to pass the map to executemodifications or something...
+			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))
-
-		cmdLogger.Debug("Command %q generated %d modifications", command.Name, 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 {
-		logger.Warning("No modifications found for file %q", file)
+		runOtherCommandsLogger.Warning("No modifications found for file")
-		return fileDataStr, nil
+		return fileDataStr, NothingToDo
 	}
+	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))
 
-	fileMutex.Lock()
+	atomic.AddInt64(&stats.TotalModifications, int64(count))
-	stats.ProcessedFiles++
-	stats.TotalModifications += count
-	fileMutex.Unlock()
 
-	logger.Info("Executed %d modifications for file %q", count, file)
+	runOtherCommandsLogger.Info("Executed %d modifications for file", count)
 	return fileDataStr, nil
 }
 
-func RunIsolateCommands(association utils.FileCommandAssociation, file string, fileDataStr string, fileMutex *sync.Mutex) (string, error) {
+func RunIsolateCommands(association utils.FileCommandAssociation, file string, fileDataStr string) (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
 	for _, isolateCommand := range association.IsolateCommands {
-		logger.Info("Processing file %q with isolate command %q", file, isolateCommand.Regex)
+		// Check if this isolate command should use JSON mode
-		modifications, err := processor.ProcessRegex(fileDataStr, isolateCommand, file)
+		if isolateCommand.JSON || *utils.JSON {
-		if err != nil {
+			runIsolateCommandsLogger.Debug("Begin processing file with JSON isolate command %q", isolateCommand.Name)
-			logger.Error("Failed to process file %q with isolate command %q: %v", file, isolateCommand.Regex, err)
+			modifications, err := processor.ProcessJSON(fileDataStr, isolateCommand, file)
-			continue
+			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
+			fileDataStr, count = utils.ExecuteModifications(modifications, fileDataStr)
+			runIsolateCommandsLogger.Trace("File data after JSON isolate modifications: %s", utils.LimitString(fileDataStr, 200))
+
+			atomic.AddInt64(&stats.TotalModifications, int64(count))
+
+			runIsolateCommandsLogger.Info("Executed %d JSON isolate modifications for file", count)
+		} else {
+			// Regular regex processing for isolate commands
+			runIsolateCommandsLogger.Debug("Begin processing file with isolate command %q", isolateCommand.Regex)
+			patterns := isolateCommand.Regexes
+			if len(patterns) == 0 {
+				patterns = []string{isolateCommand.Regex}
+			}
+			for idx, pattern := range patterns {
+				tmpCmd := isolateCommand
+				tmpCmd.Regex = pattern
+				modifications, err := processor.ProcessRegex(fileDataStr, 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
+				fileDataStr, count = utils.ExecuteModifications(modifications, fileDataStr)
+				runIsolateCommandsLogger.Trace("File data after isolate modifications: %s", utils.LimitString(fileDataStr, 200))
+
+				atomic.AddInt64(&stats.TotalModifications, int64(count))
+
+				runIsolateCommandsLogger.Info("Executed %d isolate modifications for file", count)
+			}
 		}
-
+	}
-		if len(modifications) == 0 {
+	if !anythingDone {
-			logger.Warning("No modifications found for file %q", file)
+		runIsolateCommandsLogger.Debug("No isolate modifications were made for file")
-			continue
+		return fileDataStr, NothingToDo
-		}
-
-		var count int
-		fileDataStr, count = utils.ExecuteModifications(modifications, fileDataStr)
-
-		fileMutex.Lock()
-		stats.ProcessedFiles++
-		stats.TotalModifications += count
-		fileMutex.Unlock()
-
-		logger.Info("Executed %d isolate modifications for file %q", count, file)
 	}
 	return fileDataStr, nil
 }

processor/json.go

@@ -0,0 +1,656 @@
+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)
+	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
+}
+
+// applyJSONChanges compares original and modified data and applies changes surgically
+func applyJSONChanges(content string, originalData, modifiedData interface{}) ([]utils.ReplaceCommand, error) {
+	var commands []utils.ReplaceCommand
+
+	appliedCommands, err := applyChanges(content, originalData, modifiedData)
+	if err == nil && len(appliedCommands) > 0 {
+		return appliedCommands, nil
+	}
+
+	return commands, fmt.Errorf("failed to make any changes to the json")
+}
+
+// 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
+	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 {
+					// Elements added - more complex, skip for now
+				}
+			} 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
+							}
+						}
+					}
+				}
+			}
+		}
+	default:
+		// For primitive types, compare directly
+		if !deepEqual(original, modified) {
+			if basePath == "" {
+				changes[""] = modified
+			} else {
+				changes[basePath] = modified
+			}
+		}
+	}
+
+	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{} to a Lua table recursively
+func ToLuaTable(L *lua.LState, data interface{}) (*lua.LTable, error) {
+	toLuaTableLogger := jsonLogger.WithPrefix("ToLuaTable")
+	toLuaTableLogger.Debug("Converting Go interface to Lua table")
+	toLuaTableLogger.Trace("Input data type: %T", data)
+
+	switch v := data.(type) {
+	case map[string]interface{}:
+		toLuaTableLogger.Debug("Converting map to Lua table")
+		table := L.CreateTable(0, len(v))
+		for key, value := range v {
+			luaValue, err := ToLuaValue(L, value)
+			if err != nil {
+				toLuaTableLogger.Error("Failed to convert map value for key %q: %v", key, err)
+				return nil, err
+			}
+			table.RawSetString(key, luaValue)
+		}
+		return table, nil
+
+	case []interface{}:
+		toLuaTableLogger.Debug("Converting slice to Lua table")
+		table := L.CreateTable(len(v), 0)
+		for i, value := range v {
+			luaValue, err := ToLuaValue(L, value)
+			if err != nil {
+				toLuaTableLogger.Error("Failed to convert slice value at index %d: %v", i, err)
+				return nil, err
+			}
+			table.RawSetInt(i+1, luaValue) // Lua arrays are 1-indexed
+		}
+		return table, nil
+
+	case string:
+		toLuaTableLogger.Debug("Converting string to Lua string")
+		return nil, fmt.Errorf("expected table or array, got string")
+
+	case float64:
+		toLuaTableLogger.Debug("Converting float64 to Lua number")
+		return nil, fmt.Errorf("expected table or array, got number")
+
+	case bool:
+		toLuaTableLogger.Debug("Converting bool to Lua boolean")
+		return nil, fmt.Errorf("expected table or array, got boolean")
+
+	case nil:
+		toLuaTableLogger.Debug("Converting nil to Lua nil")
+		return nil, fmt.Errorf("expected table or array, got nil")
+
+	default:
+		toLuaTableLogger.Error("Unsupported type for Lua table conversion: %T", v)
+		return nil, fmt.Errorf("unsupported type for Lua table conversion: %T", v)
+	}
+}
+
+// ToLuaValue converts a Go interface{} to a Lua value
+func ToLuaValue(L *lua.LState, data interface{}) (lua.LValue, error) {
+	toLuaValueLogger := jsonLogger.WithPrefix("ToLuaValue")
+	toLuaValueLogger.Debug("Converting Go interface to Lua value")
+	toLuaValueLogger.Trace("Input data type: %T", data)
+
+	switch v := data.(type) {
+	case map[string]interface{}:
+		toLuaValueLogger.Debug("Converting map to Lua table")
+		table := L.CreateTable(0, len(v))
+		for key, value := range v {
+			luaValue, err := ToLuaValue(L, value)
+			if err != nil {
+				toLuaValueLogger.Error("Failed to convert map value for key %q: %v", key, err)
+				return lua.LNil, err
+			}
+			table.RawSetString(key, luaValue)
+		}
+		return table, nil
+
+	case []interface{}:
+		toLuaValueLogger.Debug("Converting slice to Lua table")
+		table := L.CreateTable(len(v), 0)
+		for i, value := range v {
+			luaValue, err := ToLuaValue(L, value)
+			if err != nil {
+				toLuaValueLogger.Error("Failed to convert slice value at index %d: %v", i, err)
+				return lua.LNil, err
+			}
+			table.RawSetInt(i+1, luaValue) // Lua arrays are 1-indexed
+		}
+		return table, nil
+
+	case string:
+		toLuaValueLogger.Debug("Converting string to Lua string")
+		return lua.LString(v), nil
+
+	case float64:
+		toLuaValueLogger.Debug("Converting float64 to Lua number")
+		return lua.LNumber(v), nil
+
+	case bool:
+		toLuaValueLogger.Debug("Converting bool to Lua boolean")
+		return lua.LBool(v), nil
+
+	case nil:
+		toLuaValueLogger.Debug("Converting nil to Lua nil")
+		return lua.LNil, nil
+
+	default:
+		toLuaValueLogger.Error("Unsupported type for Lua value conversion: %T", v)
+		return lua.LNil, fmt.Errorf("unsupported type for Lua value conversion: %T", v)
+	}
+}

processor/json_test.go

@@ -0,0 +1,96 @@
+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, err := ToLuaValue(L, tt.input)
+			assert.NoError(t, err)
+			assert.Equal(t, tt.expected, result.String())
+		})
+	}
+}

processor/processor.go

@@ -4,153 +4,145 @@ import (
 	"fmt"
 	"io"
 	"net/http"
+	"regexp"
 	"strings"
 
+	"cook/utils"
+
 	logger "git.site.quack-lab.dev/dave/cylogger"
 	lua "github.com/yuin/gopher-lua"
 )
 
+// 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)
 	}
 
@@ -158,13 +150,15 @@ 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
@@ -245,26 +239,22 @@ 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, "/") ||
@@ -273,30 +263,32 @@ 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
 }
 
 // BuildLuaScript prepares a Lua expression from shorthand notation
 func BuildLuaScript(luaExpr string) string {
-	logger.Debug("Building Lua script from expression: %s", luaExpr)
+	buildLuaScriptLogger := processorLogger.WithPrefix("BuildLuaScript").WithField("inputLuaExpr", luaExpr)
+	buildLuaScriptLogger.Debug("Building full Lua script from expression")
+
+	// 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
@@ -304,11 +296,60 @@ 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) string {
+	buildJsonLuaScriptLogger := processorLogger.WithPrefix("BuildJSONLuaScript").WithField("inputLuaExpr", luaExpr)
+	buildJsonLuaScriptLogger.Debug("Building full Lua script for JSON mode from expression")
+
+	// 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)
@@ -322,20 +363,26 @@ 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 string = "GET"
@@ -345,30 +392,38 @@ func fetch(L *lua.LState) int {
 	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
@@ -378,24 +433,33 @@ func fetch(L *lua.LState) int {
 	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 resp.Body.Close()
+	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()
@@ -403,14 +467,101 @@ func fetch(L *lua.LState) int {
 	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")
+
+	defer func() {
+		if r := recover(); r != nil {
+			evalRegexLogger.Error("Panic in EvalRegex: %v", r)
+			// Push empty table on panic
+			emptyTable := L.NewTable()
+			L.Push(emptyTable)
+		}
+	}()
+
+	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))
+
+	matchesTable := L.NewTable()
+	for i, match := range matches {
+		matchesTable.RawSetInt(i, lua.LString(match))
+		evalRegexLogger.Debug("Set table[%d] = %q", i, match)
+	}
+
+	L.Push(matchesTable)
+	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)
+  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:
+  DumpTable(table, depth) - Prints table structure recursively
+  isArray(t)          - Returns true if table is a sequential array
+
+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:
+  round(3.14159, 2)   -> 3.14
+  strsplit("a,b,c", ",") -> {"a", "b", "c"}
+  upper("hello")      -> "HELLO"
+  min(5, 3)           -> 3
+  num("123")          -> 123
+  is_number("abc")    -> false
+  fetch("https://api.example.com/data")
+  re("(\\w+)@(\\w+)", "user@domain.com") -> {"user@domain.com", "user", "domain.com"}`
+}

processor/processor_test.go

@@ -0,0 +1,162 @@
+package processor_test
+
+import (
+	"fmt"
+	"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, 0, result, "Expected return value to be 0")
+
+	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.RawGetString(fmt.Sprintf("%d", i))
+		assert.Equal(t, lua.LString(v), val, "Expected index %d to be %q", i, v)
+	}
+}
+
+// Happy Path: Function returns an empty Lua table when regex pattern does not match input string.
+func TestEvalRegex_NoMatchReturnsEmptyTable(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, 0, result)
+
+	out := L.Get(-1)
+	tbl, ok := out.(*lua.LTable)
+	if !ok {
+		t.Fatalf("Expected Lua table, got %T", out)
+	}
+	count := 0
+	tbl.ForEach(func(k, v lua.LValue) {
+		count++
+	})
+	assert.Zero(t, count, "Expected no items in the table for non-matching input")
+}
+
+// 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, 0, result)
+
+	out := L.Get(-1)
+	tbl, ok := out.(*lua.LTable)
+	if !ok {
+		t.Fatalf("Expected Lua table, got %T", out)
+	}
+	fullMatch := tbl.RawGetString("0")
+	assert.Equal(t, lua.LString("foo123"), fullMatch)
+	// There should be only the full match (index 0)
+	count := 0
+	tbl.ForEach(func(k, v lua.LValue) {
+		count++
+	})
+	assert.Equal(t, 1, count)
+}
+
+// Edge Case: Function panics or errors when given an invalid regex pattern.
+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"))
+
+	defer func() {
+		if r := recover(); r == nil {
+			t.Error("Expected panic for invalid regex pattern, but did not panic")
+		}
+	}()
+	processor.EvalRegex(L)
+}
+
+// Edge Case: Function returns an empty Lua table when input string is empty.
+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, 0, result)
+
+	out := L.Get(-1)
+	tbl, ok := out.(*lua.LTable)
+	if !ok {
+		t.Fatalf("Expected Lua table, got %T", out)
+	}
+	// Should be empty
+	count := 0
+	tbl.ForEach(func(k, v lua.LValue) {
+		count++
+	})
+	assert.Zero(t, count, "Expected empty table when input is empty")
+}
+
+// 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) {
+	// 23:47:35.567068 processor.go:369          [g:22  ] [LUA]     Pistol_Round ^((Bulk_)?(Pistol|Rifle).*?Round.*?)$
+	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)
+	}
+	count := 0
+	tbl.ForEach(func(k, v lua.LValue) {
+		fmt.Println(k, v)
+		count++
+	})
+	assert.Equal(t, 1, count)
+}

processor/regex.go

@@ -12,6 +12,9 @@ import (
 	lua "github.com/yuin/gopher-lua"
 )
 
+// regexLogger is a scoped logger for the processor/regex package.
+var regexLogger = logger.Default.WithPrefix("processor/regex")
+
 type CaptureGroup struct {
 	Name    string
 	Value   string
@@ -23,52 +26,59 @@ type CaptureGroup struct {
 // 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) {
-	var commands []utils.ReplaceCommand
+	processRegexLogger := regexLogger.WithPrefix("ProcessRegex").WithField("commandName", command.Name).WithField("file", filename)
-	logger.Trace("Processing regex: %q", command.Regex)
+	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)
+	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)
-	logger.Debug("Compiling regex pattern: %s", 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", time.Since(patternCompileStart))
 
 	// 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
+	previousLuaExpr := command.Lua
 	luaExpr := BuildLuaScript(command.Lua)
-	logger.Debug("Transformed Lua expression: %q → %q", previous, luaExpr)
+	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)
+		processRegexLogger.Warning("No matches found for regex: %q", pattern)
-		logger.Debug("Total regex processing time: %v", time.Since(startTime))
+		processRegexLogger.Debug("Total regex processing time: %v", time.Since(startTime))
 		return commands, nil
 	}
 
@@ -77,12 +87,13 @@ func ProcessRegex(content string, command utils.ModifyCommand, filename string)
 	// 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))
+		matchLogger := processRegexLogger.WithField("matchNum", i+1)
-		logger.Trace("Match indices: %v (match position %d-%d)", matchIndices, matchIndices[0], matchIndices[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))
@@ -90,7 +101,7 @@ func ProcessRegex(content string, command utils.ModifyCommand, filename string)
 		// 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
@@ -99,20 +110,17 @@ func ProcessRegex(content string, command utils.ModifyCommand, filename string)
 		// 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]]
+		matchContent := content[matchIndices[0]:matchIndices[1]]
-		matchPreview := match
+		matchPreview := utils.LimitString(matchContent, 50)
-		if len(match) > 50 {
+		matchLogger.Trace("Matched content: %q (length: %d)", matchPreview, len(matchContent))
-			matchPreview = match[:47] + "..."
-		}
-		logger.Trace("Matched content: %q (length: %d)", matchPreview, len(match))
 
 		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
 		}
 
@@ -123,11 +131,11 @@ func ProcessRegex(content string, command utils.ModifyCommand, filename string)
 				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
 			}
 		}
@@ -142,6 +150,7 @@ func ProcessRegex(content string, command utils.ModifyCommand, filename string)
 			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
 			}
 
@@ -154,75 +163,80 @@ func ProcessRegex(content string, command utils.ModifyCommand, filename string)
 
 			// 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)
 			}
 		}
 
 		// Use the DeduplicateGroups flag to control whether to deduplicate capture groups
 		if !command.NoDedup {
-			logger.Debug("Deduplicating capture groups as specified in command settings")
+			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",
+			matchLogger.Error("Lua script execution failed: %v\nScript: %s\nCapture Groups: %+v",
-				err, luaExpr, captureGroups)
+				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
+			replacement = matchContent
 
 			// Count groups that were actually modified
-			modifiedGroups := 0
+			modifiedGroupsCount := 0
-			for _, capture := range captureGroups {
+			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", LimitString(capture.Value, 50))
+					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",
+				matchLogger.Debug("Capture group %q scheduled for modification: %q → %q",
-					capture.Name, capture.Value, capture.Updated)
+					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
@@ -232,42 +246,57 @@ func ProcessRegex(content string, command utils.ModifyCommand, filename string)
 					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 _, kept := range accepted {
-		for _, existingGroup := range deduplicatedGroups {
+			// Overlap if start < keptEnd and end > keptStart (adjacent is allowed)
-			logger.Debug("Comparing with existing group: %s with range %v", existingGroup.Name, existingGroup.Range)
+			if group.Range[0] < kept.Range[1] && group.Range[1] > kept.Range[0] {
-			if group.Range[0] < existingGroup.Range[1] && group.Range[1] > existingGroup.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
+			groupLogger.Warning("Overlapping capture group detected and skipped.")
-			logger.Warning("Overlapping capture group: %s", group.Name)
 			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
@@ -276,105 +305,183 @@ 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
+		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")
+
 	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]
+		countStr := parts[2]
-		repetitions, _ := strconv.Atoi(count)
+		repetitions, err := strconv.Atoi(countStr)
-		return strings.Repeat(repeatedPattern+".*?", repetitions-1) + repeatedPattern
+		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 == "" {
+		groupLogger := fromLuaLogger.WithField("originalCaptureName", capture.Name).WithField("originalValue", utils.LimitString(capture.Value, 50))
-			capture.Name = fmt.Sprintf("%d", captureIndex+1)
+		groupLogger.Debug("Processing capture group to retrieve updated value")
 
-			vVarName := fmt.Sprintf("v%s", capture.Name)
+		if capture.Name == "" {
-			sVarName := fmt.Sprintf("s%s", 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
+			// Easy shit, directly use the named capture group
-			capture.Updated = L.GetGlobal(capture.Name).String()
+			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
@@ -387,5 +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/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)
+	}
+}

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 

utils/db.go

@@ -1,15 +1,18 @@
 package utils
 
 import (
-	"fmt"
 	"path/filepath"
 	"time"
 
-	"git.site.quack-lab.dev/dave/cylogger"
+	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
@@ -29,92 +32,126 @@ type DBWrapper struct {
 	db *gorm.DB
 }
 
-var db *DBWrapper
+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)
 	db, err := gorm.Open(sqlite.Open(dbFile), &gorm.Config{
 		// SkipDefaultTransaction: true,
 		PrepareStmt: true,
-		// Logger:      gormlogger.Default.LogMode(gormlogger.Silent),
+		Logger:      gormlogger.Default.LogMode(gormlogger.Silent),
 	})
 	if err != nil {
+		getDBLogger.Error("Failed to open database: %v", err)
 		return nil, err
 	}
-	db.AutoMigrate(&FileSnapshot{})
+	getDBLogger.Debug("Database opened successfully, running auto migration")
+	if err := db.AutoMigrate(&FileSnapshot{}); err != nil {
+		getDBLogger.Error("Auto migration failed: %v", err)
+		return nil, err
+	}
+	getDBLogger.Debug("Auto migration completed")
 
-	return &DBWrapper{db: db}, nil
+	globalDB = &DBWrapper{db: db}
+	getDBLogger.Debug("Database wrapper initialized")
+	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 {
-	log := cylogger.Default.WithPrefix(fmt.Sprintf("SaveFile: %q", filePath))
+	saveFileLogger := dbLogger.WithPrefix("SaveFile").WithField("filePath", filePath)
+	saveFileLogger.Debug("Attempting to save file to database")
+	saveFileLogger.Trace("File data length: %d", len(fileData))
+
 	exists, err := db.FileExists(filePath)
 	if err != nil {
-		log.Error("Error checking if file exists: %v", err)
+		saveFileLogger.Error("Error checking if file exists: %v", err)
 		return err
 	}
-	log.Debug("File exists: %t", exists)
-	// Nothing to do, file already exists
 	if exists {
-		log.Debug("File already exists, skipping save")
+		saveFileLogger.Debug("File already exists, skipping save")
 		return nil
 	}
-	log.Debug("Saving file to database")
+	saveFileLogger.Debug("Creating new file snapshot in database")
-	return db.db.Create(&FileSnapshot{
+	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.Debug("File saved successfully to database")
+	}
+	return err
 }
 
 func (db *DBWrapper) GetFile(filePath string) ([]byte, error) {
-	log := cylogger.Default.WithPrefix(fmt.Sprintf("GetFile: %q", filePath))
+	getFileLogger := dbLogger.WithPrefix("GetFile").WithField("filePath", filePath)
-	log.Debug("Getting file from database")
+	getFileLogger.Debug("Getting file from database")
 	var fileSnapshot FileSnapshot
 	err := db.db.Model(&FileSnapshot{}).Where("file_path = ?", filePath).First(&fileSnapshot).Error
 	if err != nil {
+		// Downgrade not-found to warning to avoid noisy errors during first run
+		getFileLogger.Warning("Failed to get file from database: %v", err)
 		return nil, err
 	}
-	log.Debug("File found in database")
+	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) {
-	log := cylogger.Default.WithPrefix("GetAllFiles")
+	getAllFilesLogger := dbLogger.WithPrefix("GetAllFiles")
-	log.Debug("Getting all files from database")
+	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
 	}
-	log.Debug("Found %d files in database", len(fileSnapshots))
+	getAllFilesLogger.Debug("Found %d files in database", len(fileSnapshots))
+	getAllFilesLogger.Trace("File snapshots retrieved: %v", fileSnapshots)
 	return fileSnapshots, nil
 }
 
 func (db *DBWrapper) RemoveAllFiles() error {
-	log := cylogger.Default.WithPrefix("RemoveAllFiles")
+	removeAllFilesLogger := dbLogger.WithPrefix("RemoveAllFiles")
-	log.Debug("Removing all files from database")
+	removeAllFilesLogger.Debug("Removing all files from database")
 	err := db.db.Exec("DELETE FROM file_snapshots").Error
 	if err != nil {
-		return err
+		removeAllFilesLogger.Error("Failed to remove all files from database: %v", err)
+	} else {
+		removeAllFilesLogger.Debug("All files removed from database")
 	}
-	log.Debug("All files removed from database")
+	return err
-	return nil
 }

utils/file.go

@@ -1,96 +1,152 @@
 package utils
 
 import (
-	"fmt"
 	"os"
 	"path/filepath"
+	"strconv"
 	"strings"
 
-	"git.site.quack-lab.dev/dave/cylogger"
+	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")
+
 func CleanPath(path string) string {
-	log := cylogger.Default.WithPrefix(fmt.Sprintf("CleanPath: %q", path))
+	cleanPathLogger := fileLogger.WithPrefix("CleanPath")
-	log.Trace("Start")
+	cleanPathLogger.Debug("Cleaning path: %q", path)
+	cleanPathLogger.Trace("Original path: %q", path)
 	path = filepath.Clean(path)
 	path = strings.ReplaceAll(path, "\\", "/")
-	log.Trace("Done: %q", path)
+	cleanPathLogger.Trace("Cleaned path result: %q", path)
 	return path
 }
 
 func ToAbs(path string) string {
-	log := cylogger.Default.WithPrefix(fmt.Sprintf("ToAbs: %q", path))
+	toAbsLogger := fileLogger.WithPrefix("ToAbs")
-	log.Trace("Start")
+	toAbsLogger.Debug("Converting path to absolute: %q", path)
+	toAbsLogger.Trace("Input path: %q", path)
 	if filepath.IsAbs(path) {
-		log.Trace("Path is already absolute: %q", path)
+		toAbsLogger.Debug("Path is already absolute, cleaning it.")
-		return CleanPath(path)
+		cleanedPath := CleanPath(path)
+		toAbsLogger.Trace("Already absolute path after cleaning: %q", cleanedPath)
+		return cleanedPath
 	}
 	cwd, err := os.Getwd()
 	if err != nil {
-		log.Error("Error getting cwd: %v", err)
+		toAbsLogger.Error("Error getting current working directory: %v", err)
 		return CleanPath(path)
 	}
-	log.Trace("Cwd: %q", cwd)
+	toAbsLogger.Trace("Current working directory: %q", cwd)
-	return CleanPath(filepath.Join(cwd, path))
+	cleanedPath := CleanPath(filepath.Join(cwd, path))
+	toAbsLogger.Trace("Converted absolute path result: %q", cleanedPath)
+	return cleanedPath
+}
+
+// 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
+}
+
+// StrToFloat converts a string to a float64, returning 0 on error.
+func StrToFloat(s string) float64 {
+	strToFloatLogger := fileLogger.WithPrefix("StrToFloat").WithField("inputString", s)
+	strToFloatLogger.Debug("Attempting to convert string to float")
+	f, err := strconv.ParseFloat(s, 64)
+	if err != nil {
+		strToFloatLogger.Warning("Failed to convert string %q to float, returning 0: %v", s, err)
+		return 0
+	}
+	strToFloatLogger.Trace("Successfully converted %q to float: %f", s, f)
+	return f
 }
 
 func ResetWhereNecessary(associations map[string]FileCommandAssociation, db DB) error {
-	log := cylogger.Default.WithPrefix("ResetWhereNecessary")
+	resetWhereNecessaryLogger := fileLogger.WithPrefix("ResetWhereNecessary")
-	log.Debug("Start")
+	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 {
-			log.Debug("Checking command %q for file %q", command.Name, association.File)
+			resetWhereNecessaryLogger.Debug("Checking command %q for reset requirement", command.Name)
+			resetWhereNecessaryLogger.Trace("Command details: %v", command)
 			if command.Reset {
-				log.Debug("Command %q requires reset for file %q", command.Name, association.File)
+				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 {
-			log.Debug("Checking isolate command %q for file %q", command.Name, association.File)
+			resetWhereNecessaryLogger.Debug("Checking isolate command %q for reset requirement", command.Name)
+			resetWhereNecessaryLogger.Trace("Isolate command details: %v", command)
 			if command.Reset {
-				log.Debug("Isolate command %q requires reset for file %q", command.Name, association.File)
+				resetWhereNecessaryLogger.Debug("Isolate command %q requires reset for file %q, marking as dirty", command.Name, association.File)
 				dirtyFiles[association.File] = struct{}{}
 			}
 		}
 	}
-	log.Debug("Dirty files: %v", dirtyFiles)
+	resetWhereNecessaryLogger.Debug("Identified %d files that need to be reset", len(dirtyFiles))
+	resetWhereNecessaryLogger.Trace("Dirty files identified: %v", dirtyFiles)
+
 	for file := range dirtyFiles {
-		log.Debug("Resetting file %q", file)
+		resetWhereNecessaryLogger.Debug("Resetting file %q", file)
 		fileData, err := db.GetFile(file)
 		if err != nil {
-			log.Warning("Failed to get file %q: %v", file, err)
+			resetWhereNecessaryLogger.Warning("Failed to get original content for file %q from database: %v", file, err)
-			continue
+			// 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
 		}
-		log.Debug("Writing file %q to disk", file)
+		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 {
-			log.Warning("Failed to write file %q: %v", file, err)
+			resetWhereNecessaryLogger.Warning("Failed to write original content back to file %q: %v", file, err)
 			continue
 		}
-		log.Debug("File %q written to disk", file)
+		resetWhereNecessaryLogger.Debug("Successfully reset file %q", file)
 	}
-	log.Debug("Done")
+	resetWhereNecessaryLogger.Debug("Finished reset where necessary operation")
 	return nil
 }
 
 func ResetAllFiles(db DB) error {
-	log := cylogger.Default.WithPrefix("ResetAllFiles")
+	resetAllFilesLogger := fileLogger.WithPrefix("ResetAllFiles")
-	log.Debug("Start")
+	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
 	}
-	log.Debug("Found %d files in database", len(fileSnapshots))
+	resetAllFilesLogger.Debug("Found %d files in database to reset", len(fileSnapshots))
+	resetAllFilesLogger.Trace("File snapshots retrieved: %v", fileSnapshots)
+
 	for _, fileSnapshot := range fileSnapshots {
-		log.Debug("Resetting file %q", fileSnapshot.FilePath)
+		resetAllFilesLogger.Debug("Resetting file %q", fileSnapshot.FilePath)
 		err = os.WriteFile(fileSnapshot.FilePath, fileSnapshot.FileData, 0644)
 		if err != nil {
-			log.Warning("Failed to write file %q: %v", fileSnapshot.FilePath, err)
+			resetAllFilesLogger.Warning("Failed to write file %q to disk: %v", fileSnapshot.FilePath, err)
 			continue
 		}
-		log.Debug("File %q written to disk", fileSnapshot.FilePath)
+		resetAllFilesLogger.Debug("File %q written to disk successfully", fileSnapshot.FilePath)
 	}
-	log.Debug("Done")
+	resetAllFilesLogger.Debug("Finished reset all files operation")
 	return nil
 }

utils/flags.go

@@ -2,9 +2,20 @@ package utils
 
 import (
 	"flag"
+
+	logger "git.site.quack-lab.dev/dave/cylogger"
 )
 
+// flagsLogger is a scoped logger for the utils/flags package.
+var flagsLogger = logger.Default.WithPrefix("utils/flags")
+
 var (
 	ParallelFiles = flag.Int("P", 100, "Number of files to process in parallel")
 	Filter        = flag.String("f", "", "Filter commands before running them")
+	JSON          = flag.Bool("json", false, "Enable JSON mode for processing JSON files")
 )
+
+func init() {
+	flagsLogger.Debug("Initializing flags")
+	flagsLogger.Trace("ParallelFiles initial value: %d, Filter initial value: %q, JSON initial value: %t", *ParallelFiles, *Filter, *JSON)
+}

utils/modifycommand.go

@@ -11,32 +11,51 @@ import (
 	"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"`
+	Name      string                 `yaml:"name,omitempty"`
-	Regex    string   `yaml:"regex"`
+	Regex     string                 `yaml:"regex,omitempty"`
-	Lua      string   `yaml:"lua"`
+	Regexes   []string               `yaml:"regexes,omitempty"`
-	Files    []string `yaml:"files"`
+	Lua       string                 `yaml:"lua,omitempty"`
-	Reset    bool     `yaml:"reset"`
+	Files     []string               `yaml:"files,omitempty"`
-	LogLevel string   `yaml:"loglevel"`
+	Reset     bool                   `yaml:"reset,omitempty"`
-	Isolate  bool     `yaml:"isolate"`
+	LogLevel  string                 `yaml:"loglevel,omitempty"`
-	NoDedup  bool     `yaml:"nodedup"`
+	Isolate   bool                   `yaml:"isolate,omitempty"`
-	Disabled bool     `yaml:"disable"`
+	NoDedup   bool                   `yaml:"nodedup,omitempty"`
+	Disabled  bool                   `yaml:"disable,omitempty"`
+	JSON      bool                   `yaml:"json,omitempty"`
+	Modifiers map[string]interface{} `yaml:"modifiers,omitempty"`
 }
+
 type CookFile []ModifyCommand
 
 func (c *ModifyCommand) Validate() error {
-	if c.Regex == "" {
+	validateLogger := modifyCommandLogger.WithPrefix("Validate").WithField("commandName", c.Name)
-		return fmt.Errorf("pattern is required")
+	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
 }
 
@@ -44,34 +63,47 @@ func (c *ModifyCommand) Validate() error {
 var matchesMemoTable map[string]bool = make(map[string]bool)
 
 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 {
-		logger.Debug("Found match for file %q and glob %q in memo table", path, glob)
+		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)
 	static, pattern := doublestar.SplitPattern(pattern)
 
 	cwd, err := os.Getwd()
 	if err != nil {
+		splitPatternLogger.Error("Error getting current working directory: %v", err)
 		return "", ""
 	}
+	splitPatternLogger.Trace("Current working directory: %q", cwd)
 	if static == "" {
+		splitPatternLogger.Debug("Static part is empty, defaulting to current working directory")
 		static = cwd
 	}
 	if !filepath.IsAbs(static) {
+		splitPatternLogger.Debug("Static part is not absolute, joining with current working directory")
 		static = filepath.Join(cwd, static)
 		static = filepath.Clean(static)
+		splitPatternLogger.Trace("Static path after joining and cleaning: %q", static)
 	}
 	static = strings.ReplaceAll(static, "\\", "/")
+	splitPatternLogger.Trace("Final static path: %q, Remaining pattern: %q", static, pattern)
 	return static, pattern
 }
 
@@ -82,180 +114,262 @@ type FileCommandAssociation struct {
 }
 
 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]FileCommandAssociation)
 
 	for _, file := range files {
 		file = strings.ReplaceAll(file, "\\", "/")
+		associateFilesLogger.Debug("Processing file: %q", file)
 		fileCommands[file] = FileCommandAssociation{
 			File:            file,
 			IsolateCommands: []ModifyCommand{},
 			Commands:        []ModifyCommand{},
 		}
 		for _, command := range commands {
+			associateFilesLogger.Debug("Checking command %q for file %q", command.Name, file)
 			for _, glob := range command.Files {
 				glob = strings.ReplaceAll(glob, "\\", "/")
 				static, pattern := SplitPattern(glob)
-				patternFile := strings.Replace(file, static+`/`, "", 1)
+				associateFilesLogger.Trace("Glob parts for %q → static=%q pattern=%q", glob, static, pattern)
+
+				// Build absolute path for the current file to compare with static
+				cwd, err := os.Getwd()
+				if err != nil {
+					associateFilesLogger.Warning("Failed to get CWD when matching %q for file %q: %v", glob, file, err)
+					continue
+				}
+				var absFile string
+				if filepath.IsAbs(file) {
+					absFile = filepath.Clean(file)
+				} else {
+					absFile = filepath.Clean(filepath.Join(cwd, file))
+				}
+				absFile = strings.ReplaceAll(absFile, "\\", "/")
+				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)
+					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].Commands), file)
+		currentFileCommands := fileCommands[file]
-		if len(fileCommands[file].Commands) == 0 {
+		associateFilesLogger.Debug("Finished processing file %q. Found %d regular commands and %d isolate commands", file, len(currentFileCommands.Commands), len(currentFileCommands.IsolateCommands))
-			logger.Info("No commands found for file %q", file)
+		associateFilesLogger.Trace("Commands for file %q: %v", file, currentFileCommands.Commands)
-		}
+		associateFilesLogger.Trace("Isolate commands for file %q: %v", file, currentFileCommands.IsolateCommands)
-		if len(fileCommands[file].IsolateCommands) > 0 {
-			logger.Info("Found %d isolate commands for file %q", len(fileCommands[file].IsolateCommands), file)
-		}
 	}
-	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 {
-			glob = strings.Replace(glob, "~", os.Getenv("HOME"), 1)
+			resolvedGlob := strings.Replace(glob, "~", os.Getenv("HOME"), 1)
-			glob = strings.ReplaceAll(glob, "\\", "/")
+			resolvedGlob = strings.ReplaceAll(resolvedGlob, "\\", "/")
-			globs[glob] = struct{}{}
+			aggregateGlobsLogger.Trace("Adding glob: %q (resolved to %q)", glob, resolvedGlob)
+			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) {
+	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)
+		expandGlobsLogger.Debug("Processing glob pattern: %q", pattern)
 		static, pattern := SplitPattern(pattern)
-		matches, _ := doublestar.Glob(os.DirFS(static), pattern)
+		matches, err := doublestar.Glob(os.DirFS(static), pattern)
-		logger.Debug("Found %d matches for pattern %s", len(matches), pattern)
+		if err != nil {
+			expandGlobsLogger.Warning("Error expanding glob %q in %q: %v", pattern, static, err)
+			continue
+		}
+		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 {
 			m = filepath.Join(static, m)
 			info, err := os.Stat(m)
 			if err != nil {
-				logger.Warning("Error getting file info for %s: %v", m, err)
+				expandGlobsLogger.Warning("Error getting file info for %q: %v", m, err)
 				continue
 			}
 			if !info.IsDir() && !filesMap[m] {
-				logger.Trace("Adding file to process list: %s", m)
+				expandGlobsLogger.Trace("Adding unique file to list: %q", m)
 				filesMap[m], files = true, append(files, m)
 			}
 		}
 	}
 
 	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) {
+	loadCommandsLogger := modifyCommandLogger.WithPrefix("LoadCommands")
+	loadCommandsLogger.Debug("Loading commands from arguments (cook files or direct patterns)")
+	loadCommandsLogger.Trace("Input arguments: %v", args)
 	commands := []ModifyCommand{}
 
-	logger.Info("Loading commands from cook files: %s", args)
 	for _, arg := range args {
-		newcommands, err := LoadCommandsFromCookFiles(arg)
+		loadCommandsLogger.Debug("Processing argument for commands: %q", arg)
+		newCommands, err := LoadCommandsFromCookFiles(arg)
 		if err != nil {
+			loadCommandsLogger.Error("Failed to load commands from argument %q: %v", arg, err)
 			return nil, fmt.Errorf("failed to load commands from cook files: %w", err)
 		}
-		logger.Info("Successfully loaded %d commands from cook files", len(newcommands))
+		loadCommandsLogger.Debug("Successfully loaded %d commands from %q", len(newCommands), arg)
-		for _, cmd := range newcommands {
+		for _, cmd := range newCommands {
 			if cmd.Disabled {
-				logger.Info("Skipping disabled command: %s", cmd.Name)
+				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))
 		}
-		logger.Info("Now total commands: %d", len(commands))
 	}
 
-	logger.Info("Loaded %d commands from all cook file", len(commands))
+	loadCommandsLogger.Info("Finished loading commands. Total %d commands loaded", len(commands))
 	return commands, nil
 }
 
 func LoadCommandsFromCookFiles(pattern string) ([]ModifyCommand, 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(static), pattern)
 	if err != nil {
+		loadCookFilesLogger.Error("Failed to glob cook files for pattern %q: %v", pattern, err)
 		return 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 {
 		cookFile = filepath.Join(static, cookFile)
 		cookFile = filepath.Clean(cookFile)
 		cookFile = strings.ReplaceAll(cookFile, "\\", "/")
-		logger.Info("Loading commands from cook file: %s", cookFile)
+		loadCookFilesLogger.Debug("Loading commands from individual cook file: %q", cookFile)
 
 		cookFileData, err := os.ReadFile(cookFile)
 		if err != nil {
+			loadCookFilesLogger.Error("Failed to read cook file %q: %v", cookFile, err)
 			return 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, err := LoadCommandsFromCookFile(cookFileData)
 		if err != nil {
+			loadCookFilesLogger.Error("Failed to load commands from cook file data for %q: %v", cookFile, err)
 			return nil, fmt.Errorf("failed to load commands from cook file: %w", err)
 		}
-		commands = append(commands, newcommands...)
+		commands = append(commands, newCommands...)
+		loadCookFilesLogger.Debug("Added %d commands from cook file %q. Total commands now: %d", len(newCommands), cookFile, len(commands))
 	}
 
+	loadCookFilesLogger.Debug("Finished loading commands from cook files. Total %d commands", len(commands))
 	return commands, nil
 }
 
 func LoadCommandsFromCookFile(cookFileData []byte) ([]ModifyCommand, error) {
+	loadCommandLogger := modifyCommandLogger.WithPrefix("LoadCommandsFromCookFile")
+	loadCommandLogger.Debug("Unmarshaling commands from cook file data")
+	loadCommandLogger.Trace("Cook file data length: %d", len(cookFileData))
 	commands := []ModifyCommand{}
 	err := yaml.Unmarshal(cookFileData, &commands)
 	if err != nil {
+		loadCommandLogger.Error("Failed to unmarshal cook file data: %v", err)
 		return nil, fmt.Errorf("failed to unmarshal cook file: %w", err)
 	}
+	loadCommandLogger.Debug("Successfully unmarshaled %d commands", len(commands))
+	loadCommandLogger.Trace("Unmarshaled commands: %v", commands)
 	return commands, 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 {
-		for _, filter := range filters {
+		filterCommandsLogger.Debug("Checking command %q against filters", cmd.Name)
-			if strings.Contains(cmd.Name, filter) {
+		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
 }

utils/replacecommand.go

@@ -7,6 +7,9 @@ import (
 	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
@@ -14,45 +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)
+	executeLogger.Trace("Applying replacement: fileDataStr[:%d] + %q + fileDataStr[%d:]", m.From, m.With, m.To)
-	return fileDataStr[:m.From] + m.With + fileDataStr[m.To:], nil
+	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
 }