Hallucinate a json mode implementation

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

@@ -1,2 +1,4 @@
 *.exe
 .qodo
+*.sqlite
+testfiles

.vscode/launch.json

@@ -12,11 +12,23 @@
 			"program": "${workspaceFolder}",
 			"cwd": "C:/Users/Administrator/Seafile/Games-Barotrauma",
 			"args": [
-				"loglevel",
+				"-loglevel",
 				"trace",
-				"(?-s)LightComponent!anyrange=\"(!num)\"",
+				"-cook",
-				"*4",
+				"*.yml",
-				"**/Outpost*.xml"
+			]
+		},
+		{
+			"name": "Launch Package (Payday 2)",
+			"type": "go",
+			"request": "launch",
+			"mode": "auto",
+			"program": "${workspaceFolder}",
+			"cwd": "C:/Users/Administrator/Seafile/Games-Payday2",
+			"args": [
+				"-loglevel",
+				"trace",
+				"*.yml",
 			]
 		},
 		{
@@ -33,6 +45,28 @@
 				"cookassistant.yml",
 			]
 		},
+		{
+			"name": "Launch Package (Quasimorph cookfile)",
+			"type": "go",
+			"request": "launch",
+			"mode": "auto",
+			"program": "${workspaceFolder}",
+			"cwd": "C:/Users/Administrator/Seafile/Games-Quasimorph",
+			"args": [
+				"cook.yml",
+			]
+		},
+		{
+			"name": "Launch Package (Rimworld cookfile)",
+			"type": "go",
+			"request": "launch",
+			"mode": "auto",
+			"program": "${workspaceFolder}",
+			"cwd": "C:/Users/Administrator/Seafile/Games-Rimworld/294100",
+			"args": [
+				"cookVehicles.yml",
+			]
+		},
 		{
 			"name": "Launch Package (Workspace)",
 			"type": "go",
@@ -40,11 +74,29 @@
 			"mode": "auto",
 			"program": "${workspaceFolder}",
 			"args": [
-				"-loglevel",
+				"tester.yml",
-				"trace",
+			]
-				"(?-s)LightComponent!anyrange=\"(!num)\"",
+		},
-				"*4",
+		{
-				"**/Outpost*.xml"
+			"name": "Launch Package (Avorion)",
+			"type": "go",
+			"request": "launch",
+			"mode": "auto",
+			"program": "${workspaceFolder}",
+			"cwd": "C:/Users/Administrator/Seafile/Games-Avorion/Avorion",
+			"args": [
+				"*.yml",
+			]
+		},
+		{
+			"name": "Launch Package (Minecraft)",
+			"type": "go",
+			"request": "launch",
+			"mode": "auto",
+			"program": "${workspaceFolder}",
+			"cwd": "C:/Users/Administrator/Seafile/Games-Minecraft",
+			"args": [
+				"cook_tacz.yml",
 			]
 		}
 	]

cmd/log_format_test/main.go

@@ -1,8 +1,9 @@
 package main
 
 import (
-	"modify/logger"
 	"time"
+
+	logger "git.site.quack-lab.dev/dave/cylogger"
 )
 
 func main() {

glob_test.go

@@ -1,7 +1,7 @@
 package main
 
 import (
-	"modify/utils"
+	"cook/utils"
 	"os"
 	"path/filepath"
 	"testing"

go.mod

@@ -1,38 +1,32 @@
-module modify
+module cook
 
-go 1.24.1
+go 1.23.2
 
 require (
+	git.site.quack-lab.dev/dave/cylogger v1.3.0
 	github.com/bmatcuk/doublestar/v4 v4.8.1
 	github.com/stretchr/testify v1.10.0
 	github.com/yuin/gopher-lua v1.1.1
 	gopkg.in/yaml.v3 v3.0.1
+	gorm.io/gorm v1.30.0
 )
 
 require (
-	dario.cat/mergo v1.0.0 // indirect
-	github.com/Microsoft/go-winio v0.6.2 // indirect
-	github.com/ProtonMail/go-crypto v1.1.5 // indirect
-	github.com/cloudflare/circl v1.6.0 // indirect
-	github.com/cyphar/filepath-securejoin v0.4.1 // indirect
 	github.com/davecgh/go-spew v1.1.1 // indirect
-	github.com/emirpasic/gods v1.18.1 // indirect
+	github.com/google/go-cmp v0.6.0 // indirect
-	github.com/go-git/gcfg v1.5.1-0.20230307220236-3a3c6141e376 // indirect
+	github.com/hexops/valast v1.5.0 // indirect
-	github.com/go-git/go-billy/v5 v5.6.2 // indirect
+	github.com/jinzhu/inflection v1.0.0 // indirect
-	github.com/jbenet/go-context v0.0.0-20150711004518-d14ea06fba99 // indirect
+	github.com/jinzhu/now v1.1.5 // indirect
-	github.com/kevinburke/ssh_config v1.2.0 // indirect
+	github.com/kr/pretty v0.3.1 // indirect
-	github.com/pjbgf/sha1cd v0.3.2 // indirect
+	github.com/mattn/go-sqlite3 v1.14.22 // indirect
 	github.com/pmezard/go-difflib v1.0.0 // indirect
-	github.com/sergi/go-diff v1.3.2-0.20230802210424-5b0b94c5c0d3 // indirect
+	github.com/rogpeppe/go-internal v1.14.1 // indirect
-	github.com/skeema/knownhosts v1.3.1 // indirect
+	golang.org/x/mod v0.21.0 // indirect
-	github.com/xanzy/ssh-agent v0.3.3 // indirect
+	golang.org/x/sync v0.11.0 // indirect
-	golang.org/x/crypto v0.35.0 // indirect
+	golang.org/x/text v0.22.0 // indirect
-	golang.org/x/sys v0.30.0 // indirect
+	golang.org/x/tools v0.26.0 // indirect
-	gopkg.in/warnings.v0 v0.1.2 // indirect
+	gopkg.in/check.v1 v1.0.0-20201130134442-10cb98267c6c // indirect
+	mvdan.cc/gofumpt v0.4.0 // indirect
 )
 
-require (
+require gorm.io/driver/sqlite v1.6.0
-	github.com/go-git/go-git/v5 v5.14.0
-	github.com/golang/groupcache v0.0.0-20241129210726-2c02b8208cf8 // indirect
-	golang.org/x/net v0.35.0 // indirect
-)

go.sum

@@ -1,106 +1,59 @@
-dario.cat/mergo v1.0.0 h1:AGCNq9Evsj31mOgNPcLyXc+4PNABt905YmuqPYYpBWk=
+git.site.quack-lab.dev/dave/cylogger v1.3.0 h1:eTWPUD+ThVi8kGIsRcE0XDeoH3yFb5miFEODyKUdWJw=
-dario.cat/mergo v1.0.0/go.mod h1:uNxQE+84aUszobStD9th8a29P2fMDhsBdgRYvZOxGmk=
+git.site.quack-lab.dev/dave/cylogger v1.3.0/go.mod h1:wctgZplMvroA4X6p8f4B/LaCKtiBcT1Pp+L14kcS8jk=
-github.com/Microsoft/go-winio v0.5.2/go.mod h1:WpS1mjBmmwHBEWmogvA2mj8546UReBk4v8QkMxJ6pZY=
-github.com/Microsoft/go-winio v0.6.2 h1:F2VQgta7ecxGYO8k3ZZz3RS8fVIXVxONVUPlNERoyfY=
-github.com/Microsoft/go-winio v0.6.2/go.mod h1:yd8OoFMLzJbo9gZq8j5qaps8bJ9aShtEA8Ipt1oGCvU=
-github.com/ProtonMail/go-crypto v1.1.5 h1:eoAQfK2dwL+tFSFpr7TbOaPNUbPiJj4fLYwwGE1FQO4=
-github.com/ProtonMail/go-crypto v1.1.5/go.mod h1:rA3QumHc/FZ8pAHreoekgiAbzpNsfQAosU5td4SnOrE=
-github.com/anmitsu/go-shlex v0.0.0-20200514113438-38f4b401e2be h1:9AeTilPcZAjCFIImctFaOjnTIavg87rW78vTPkQqLI8=
-github.com/anmitsu/go-shlex v0.0.0-20200514113438-38f4b401e2be/go.mod h1:ySMOLuWl6zY27l47sB3qLNK6tF2fkHG55UZxx8oIVo4=
-github.com/armon/go-socks5 v0.0.0-20160902184237-e75332964ef5 h1:0CwZNZbxp69SHPdPJAN/hZIm0C4OItdklCFmMRWYpio=
-github.com/armon/go-socks5 v0.0.0-20160902184237-e75332964ef5/go.mod h1:wHh0iHkYZB8zMSxRWpUBQtwG5a7fFgvEO+odwuTv2gs=
 github.com/bmatcuk/doublestar/v4 v4.8.1 h1:54Bopc5c2cAvhLRAzqOGCYHYyhcDHsFF4wWIR5wKP38=
 github.com/bmatcuk/doublestar/v4 v4.8.1/go.mod h1:xBQ8jztBU6kakFMg+8WGxn0c6z1fTSPVIjEY1Wr7jzc=
-github.com/cloudflare/circl v1.6.0 h1:cr5JKic4HI+LkINy2lg3W2jF8sHCVTBncJr5gIIq7qk=
+github.com/creack/pty v1.1.9/go.mod h1:oKZEueFk5CKHvIhNR5MUki03XCEU+Q6VDXinZuGJ33E=
-github.com/cloudflare/circl v1.6.0/go.mod h1:uddAzsPgqdMAYatqJ0lsjX1oECcQLIlRpzZh3pJrofs=
-github.com/cyphar/filepath-securejoin v0.4.1 h1:JyxxyPEaktOD+GAnqIqTf9A8tHyAG22rowi7HkoSU1s=
-github.com/cyphar/filepath-securejoin v0.4.1/go.mod h1:Sdj7gXlvMcPZsbhwhQ33GguGLDGQL7h7bg04C/+u9jI=
-github.com/davecgh/go-spew v1.1.0/go.mod h1:J7Y8YcW2NihsgmVo/mv3lAwl/skON4iLHjSsI+c5H38=
 github.com/davecgh/go-spew v1.1.1 h1:vj9j/u1bqnvCEfJOwUhtlOARqs3+rkHYY13jYWTU97c=
 github.com/davecgh/go-spew v1.1.1/go.mod h1:J7Y8YcW2NihsgmVo/mv3lAwl/skON4iLHjSsI+c5H38=
-github.com/elazarl/goproxy v1.7.2 h1:Y2o6urb7Eule09PjlhQRGNsqRfPmYI3KKQLFpCAV3+o=
+github.com/frankban/quicktest v1.14.3 h1:FJKSZTDHjyhriyC81FLQ0LY93eSai0ZyR/ZIkd3ZUKE=
-github.com/elazarl/goproxy v1.7.2/go.mod h1:82vkLNir0ALaW14Rc399OTTjyNREgmdL2cVoIbS6XaE=
+github.com/frankban/quicktest v1.14.3/go.mod h1:mgiwOwqx65TmIk1wJ6Q7wvnVMocbUorkibMOrVTHZps=
-github.com/emirpasic/gods v1.18.1 h1:FXtiHYKDGKCW2KzwZKx0iC0PQmdlorYgdFG9jPXJ1Bc=
+github.com/google/go-cmp v0.6.0 h1:ofyhxvXcZhMsU5ulbFiLKl/XBFqE1GSq7atu8tAmTRI=
-github.com/emirpasic/gods v1.18.1/go.mod h1:8tpGGwCnJ5H4r6BWwaV6OrWmMoPhUl5jm/FMNAnJvWQ=
+github.com/google/go-cmp v0.6.0/go.mod h1:17dUlkBOakJ0+DkrSSNjCkIjxS6bF9zb3elmeNGIjoY=
-github.com/gliderlabs/ssh v0.3.8 h1:a4YXD1V7xMF9g5nTkdfnja3Sxy1PVDCj1Zg4Wb8vY6c=
+github.com/hexops/autogold v0.8.1 h1:wvyd/bAJ+Dy+DcE09BoLk6r4Fa5R5W+O+GUzmR985WM=
-github.com/gliderlabs/ssh v0.3.8/go.mod h1:xYoytBv1sV0aL3CavoDuJIQNURXkkfPA/wxQ1pL1fAU=
+github.com/hexops/autogold v0.8.1/go.mod h1:97HLDXyG23akzAoRYJh/2OBs3kd80eHyKPvZw0S5ZBY=
-github.com/go-git/gcfg v1.5.1-0.20230307220236-3a3c6141e376 h1:+zs/tPmkDkHx3U66DAb0lQFJrpS6731Oaa12ikc+DiI=
+github.com/hexops/gotextdiff v1.0.3 h1:gitA9+qJrrTCsiCl7+kh75nPqQt1cx4ZkudSTLoUqJM=
-github.com/go-git/gcfg v1.5.1-0.20230307220236-3a3c6141e376/go.mod h1:an3vInlBmSxCcxctByoQdvwPiA7DTK7jaaFDBTtu0ic=
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-github.com/go-git/go-billy/v5 v5.6.2 h1:6Q86EsPXMa7c3YZ3aLAQsMA0VlWmy43r6FHqa/UNbRM=
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-github.com/go-git/go-billy/v5 v5.6.2/go.mod h1:rcFC2rAsp/erv7CMz9GczHcuD0D32fWzH+MJAU+jaUU=
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-github.com/go-git/go-git-fixtures/v4 v4.3.2-0.20231010084843-55a94097c399 h1:eMje31YglSBqCdIqdhKBW8lokaMrL3uTkpGYlE2OOT4=
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-github.com/go-git/go-git-fixtures/v4 v4.3.2-0.20231010084843-55a94097c399/go.mod h1:1OCfN199q1Jm3HZlxleg+Dw/mwps2Wbk9frAWm+4FII=
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-github.com/go-git/go-git/v5 v5.14.0 h1:/MD3lCrGjCen5WfEAzKg00MJJffKhC8gzS80ycmCi60=
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-github.com/go-git/go-git/v5 v5.14.0/go.mod h1:Z5Xhoia5PcWA3NF8vRLURn9E5FRhSl7dGj9ItW3Wk5k=
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-github.com/golang/groupcache v0.0.0-20241129210726-2c02b8208cf8 h1:f+oWsMOmNPc8JmEHVZIycC7hBoQxHH9pNKQORJNozsQ=
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-github.com/google/go-cmp v0.7.0 h1:wk8382ETsv4JYUZwIsn6YpYiWiBsYLSJiTsyBybVuN8=
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-github.com/jbenet/go-context v0.0.0-20150711004518-d14ea06fba99/go.mod h1:1lJo3i6rXxKeerYnT8Nvf0QmHCRC1n8sfWVwXF2Frvo=
-github.com/kevinburke/ssh_config v1.2.0 h1:x584FjTGwHzMwvHx18PXxbBVzfnxogHaAReU4gf13a4=
-github.com/kevinburke/ssh_config v1.2.0/go.mod h1:CT57kijsi8u/K/BOFA39wgDQJ9CxiF4nAY/ojJ6r6mM=
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-github.com/onsi/gomega v1.34.1 h1:EUMJIKUjM8sKjYbtxQI9A4z2o+rruxnzNvpknOXie6k=
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-github.com/onsi/gomega v1.34.1/go.mod h1:kU1QgUvBDLXBJq618Xvm2LUX6rSAfRaFRTcdOeDLwwY=
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-github.com/pjbgf/sha1cd v0.3.2 h1:a9wb0bp1oC2TGwStyn0Umc/IGKQnEgF0vVaZ8QF8eo4=
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-github.com/pjbgf/sha1cd v0.3.2/go.mod h1:zQWigSxVmsHEZow5qaLtPYxpcKMMQpa09ixqBxuCS6A=
-github.com/pkg/errors v0.9.1 h1:FEBLx1zS214owpjy7qsBeixbURkuhQAwrK5UwLGTwt4=
-github.com/pkg/errors v0.9.1/go.mod h1:bwawxfHBFNV+L2hUp1rHADufV3IMtnDRdf1r5NINEl0=
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-github.com/sirupsen/logrus v1.7.0/go.mod h1:yWOB1SBYBC5VeMP7gHvWumXLIWorT60ONWic61uBYv0=
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logger/logger.go

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

logger/panic_handler.go

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

main.go

@@ -1,32 +1,35 @@
 package main
 
 import (
+	"errors"
 	"flag"
 	"fmt"
 	"os"
 	"sort"
 	"sync"
+	"sync/atomic"
 	"time"
 
-	"modify/processor"
+	"cook/processor"
-	"modify/utils"
+	"cook/utils"
 
-	"github.com/go-git/go-git/v5"
+	"gopkg.in/yaml.v3"
 
-	"modify/logger"
+	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
 }
 
 var (
-	repo     *git.Repository
-	worktree *git.Worktree
 	stats GlobalStats = GlobalStats{
 		ModificationsPerCommand: sync.Map{},
 	}
@@ -34,17 +37,20 @@ var (
 
 func main() {
 	flag.Usage = func() {
+		CreateExampleConfig()
 		fmt.Fprintf(os.Stderr, "Usage: %s [options] <pattern> <lua_expression> <...files_or_globs>\n", os.Args[0])
 		fmt.Fprintf(os.Stderr, "\nOptions:\n")
-		fmt.Fprintf(os.Stderr, "  -git\n")
-		fmt.Fprintf(os.Stderr, "        Use git to manage files\n")
 		fmt.Fprintf(os.Stderr, "  -reset\n")
 		fmt.Fprintf(os.Stderr, "        Reset files to their original state\n")
 		fmt.Fprintf(os.Stderr, "  -loglevel string\n")
 		fmt.Fprintf(os.Stderr, "        Set logging level: ERROR, WARNING, INFO, DEBUG, TRACE (default \"INFO\")\n")
+		fmt.Fprintf(os.Stderr, "  -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")
@@ -57,124 +63,240 @@ func main() {
 	flag.Parse()
 	args := flag.Args()
 
-	level := logger.ParseLevel(*utils.LogLevel)
+	logger.InitFlag()
-	logger.Init(level)
+	mainLogger.Info("Initializing with log level: %s", logger.GetLevel().String())
-	logger.Info("Initializing with log level: %s", level.String())
+	mainLogger.Trace("Full argv: %v", os.Args)
 
-	// The plan is:
+	if flag.NArg() == 0 {
-	// Load all commands
-	commands, err := utils.LoadCommands(args)
-	if err != nil {
-		logger.Error("Failed to load commands: %v", err)
 		flag.Usage()
 		return
 	}
 
+	mainLogger.Debug("Getting database connection")
+	db, err := utils.GetDB()
+	if err != nil {
+		mainLogger.Error("Failed to get database: %v", err)
+		return
+	}
+	mainLogger.Debug("Database connection established")
+
+	workdone, err := HandleSpecialArgs(args, err, db)
+	if err != nil {
+		mainLogger.Error("Failed to handle special args: %v", err)
+		return
+	}
+	if workdone {
+		mainLogger.Info("Special arguments handled, exiting.")
+		return
+	}
+
+	// The plan is:
+	// Load all commands
+	mainLogger.Debug("Loading commands from arguments")
+	mainLogger.Trace("Arguments: %v", args)
+	commands, err := utils.LoadCommands(args)
+	if err != nil || len(commands) == 0 {
+		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 {
+		mainLogger.Trace("Command: %s", command.Name)
+		if len(command.Regexes) > 0 {
+			mainLogger.Trace("Regexes: %v", command.Regexes)
+		} else {
+			mainLogger.Trace("Regex: %s", command.Regex)
+		}
+		mainLogger.Trace("Files: %v", command.Files)
+		mainLogger.Trace("Lua: %s", command.Lua)
+		mainLogger.Trace("Reset: %t", command.Reset)
+		mainLogger.Trace("Isolate: %t", command.Isolate)
+		mainLogger.Trace("LogLevel: %s", command.LogLevel)
+	}
 
 	// Resolve all the files for all the globs
-	logger.Info("Found %d unique file patterns", len(globs))
+	mainLogger.Info("Found %d unique file patterns", len(globs))
+	mainLogger.Debug("Expanding glob patterns to files")
 	files, err := utils.ExpandGLobs(globs)
 	if err != nil {
-		logger.Error("Failed to expand file patterns: %v", err)
+		mainLogger.Error("Failed to expand file patterns: %v", err)
 		return
 	}
-	logger.Info("Found %d files to process", len(files))
+	mainLogger.Info("Found %d files to process", len(files))
+	mainLogger.Trace("Files to process: %v", files)
 
 	// Somehow connect files to commands via globs..
 	// For each file check every glob of every command
 	// Maybe memoize this part
 	// That way we know what commands affect what files
+	mainLogger.Debug("Associating files with commands")
 	associations, err := utils.AssociateFilesWithCommands(files, commands)
 	if err != nil {
-		logger.Error("Failed to associate files with commands: %v", err)
+		mainLogger.Error("Failed to associate files with commands: %v", err)
 		return
 	}
+	mainLogger.Debug("Files associated with commands")
+	mainLogger.Trace("File-command associations: %v", associations)
+	// Per-file association summary for better visibility when debugging
+	for file, assoc := range associations {
+		cmdNames := make([]string, 0, len(assoc.Commands))
+		for _, c := range assoc.Commands {
+			cmdNames = append(cmdNames, c.Name)
+		}
+		isoNames := make([]string, 0, len(assoc.IsolateCommands))
+		for _, c := range assoc.IsolateCommands {
+			isoNames = append(isoNames, c.Name)
+		}
+		mainLogger.Debug("File %q has %d regular and %d isolate commands", file, len(assoc.Commands), len(assoc.IsolateCommands))
+		mainLogger.Trace("\tRegular: %v", cmdNames)
+		mainLogger.Trace("\tIsolate: %v", isoNames)
+	}
+
+	mainLogger.Debug("Resetting files where necessary")
+	err = utils.ResetWhereNecessary(associations, db)
+	if err != nil {
+		mainLogger.Error("Failed to reset files where necessary: %v", err)
+		return
+	}
+	mainLogger.Debug("Files reset where necessary")
 
 	// 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
 
-	for file, commands := range associations {
+	// Create a map to store loggers for each command
+	commandLoggers := make(map[string]*logger.Logger)
+	for _, command := range commands {
+		// Create a named logger for each command
+		cmdName := command.Name
+		if cmdName == "" {
+			// If no name is provided, use a short version of the regex pattern
+			if len(command.Regex) > 20 {
+				cmdName = command.Regex[:17] + "..."
+			} else {
+				cmdName = command.Regex
+			}
+		}
+
+		// Parse the log level for this specific command
+		cmdLogLevel := logger.ParseLevel(command.LogLevel)
+
+		// Create a logger with the command name as a field
+		commandLoggers[command.Name] = logger.Default.WithField("command", cmdName)
+		commandLoggers[command.Name].SetLevel(cmdLogLevel)
+
+		mainLogger.Debug("Created logger for command %q with log level %s", cmdName, cmdLogLevel.String())
+	}
+
+	for file, association := range associations {
 		workers <- struct{}{}
 		wg.Add(1)
 		logger.SafeGoWithArgs(func(args ...interface{}) {
 			defer func() { <-workers }()
 			defer wg.Done()
-
 			// Track per-file processing time
 			fileStartTime := time.Now()
 
+			mainLogger.Debug("Reading file %q", file)
 			fileData, err := os.ReadFile(file)
 			if err != nil {
-				logger.Error("Failed to read file %q: %v", file, err)
+				mainLogger.Error("Failed to read file %q: %v", file, err)
+				atomic.AddInt64(&stats.FailedFiles, 1)
 				return
 			}
-			logger.Trace("Loaded %d bytes of data for file %q", len(fileData), file)
 			fileDataStr := string(fileData)
+			mainLogger.Trace("File %q content: %s", file, utils.LimitString(fileDataStr, 500))
 
-			// Aggregate all the modifications and execute them
+			isChanged := false
-			modifications := []utils.ReplaceCommand{}
+			mainLogger.Debug("Running isolate commands for file %q", file)
-			for _, command := range commands {
+			fileDataStr, err = RunIsolateCommands(association, file, fileDataStr)
-				logger.Info("Processing file %q with command %q", file, command.Regex)
+			if err != nil && err != NothingToDo {
-				commands, err := processor.ProcessRegex(fileDataStr, command)
+				mainLogger.Error("Failed to run isolate commands for file %q: %v", file, err)
+				atomic.AddInt64(&stats.FailedFiles, 1)
+				return
+			}
+			if err != NothingToDo {
+				isChanged = true
+			}
+
+			mainLogger.Debug("Running other commands for file %q", file)
+			fileDataStr, err = RunOtherCommands(file, fileDataStr, association, commandLoggers)
+			if err != nil && err != NothingToDo {
+				mainLogger.Error("Failed to run other commands for file %q: %v", file, err)
+				atomic.AddInt64(&stats.FailedFiles, 1)
+				return
+			}
+			if err != NothingToDo {
+				isChanged = true
+			}
+
+			if isChanged {
+				mainLogger.Debug("Saving file %q to database", file)
+				err = db.SaveFile(file, fileData)
 				if err != nil {
-					logger.Error("Failed to process file %q with command %q: %v", file, command.Regex, err)
+					mainLogger.Error("Failed to save file %q to database: %v", file, err)
+					atomic.AddInt64(&stats.FailedFiles, 1)
 					return
 				}
-				modifications = append(modifications, commands...)
+				mainLogger.Debug("File %q saved to database", file)
-				// It is not guranteed that all the commands will be executed...
-				// TODO: Make this better
-				// We'd have to pass the map to executemodifications or something...
-				count, ok := stats.ModificationsPerCommand.Load(command.Name)
-				if !ok {
-					count = 0
-				}
-				stats.ModificationsPerCommand.Store(command.Name, count.(int)+len(commands))
 			}
 
-			if len(modifications) == 0 {
+			mainLogger.Debug("Writing file %q", file)
-				logger.Info("No modifications found for file %q", file)
-				return
-			}
-
-			// Sort commands in reverse order for safe replacements
-			fileDataStr, count := utils.ExecuteModifications(modifications, fileDataStr)
-
-			fileMutex.Lock()
-			stats.ProcessedFiles++
-			stats.TotalModifications += count
-			fileMutex.Unlock()
-
-			logger.Info("Executed %d modifications for file %q", count, file)
-
 			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?
@@ -184,44 +306,46 @@ 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))
@@ -232,10 +356,346 @@ 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 {
+			handleSpecialArgsLogger.Error("Failed to reset all files: %v", err)
+			return true, err
+		}
+		handleSpecialArgsLogger.Info("All files reset")
+		return true, nil
+	case "dump":
+		handleSpecialArgsLogger.Info("Dumping all files from database")
+		err = db.RemoveAllFiles()
+		if err != nil {
+			handleSpecialArgsLogger.Error("Failed to remove all files from database: %v", err)
+			return true, err
+		}
+		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)
+		{
+			Modifiers: map[string]interface{}{
+				"foobar":   4,
+				"multiply": 1.5,
+				"prefix":   "NEW_",
+				"enabled":  true,
+			},
+		},
+		// Multi-regex example using $variable in Lua
+		{
+			Name:    "RFToolsMultiply",
+			Regexes: []string{"generatePerTick = !num", "ticksPer\\w+ = !num", "generatorRFPerTick = !num"},
+			Lua:     "* $foobar",
+			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:  "EnableFlags",
+			Regex: `enabled\s*=\s*(true|false)`,
+			Lua:   `= $enabled`,
+			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,
+			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 {
+		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 {
+		createExampleConfigLogger.Error("Failed to write example_cook.yml: %v", err)
+		return
+	}
+
+	createExampleConfigLogger.Info("Wrote example_cook.yml")
+}
+
+var NothingToDo = errors.New("nothing to do")
+
+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 {
+		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.Debug("Processing file with JSON mode for command %q", command.Name)
+		newModifications, err := processor.ProcessJSON(fileDataStr, command, file)
+		if err != nil {
+			runOtherCommandsLogger.Error("Failed to process file with JSON command %q: %v", command.Name, err)
+			continue
+		}
+
+		// Apply JSON modifications immediately
+		if len(newModifications) > 0 {
+			var count int
+			fileDataStr, count = utils.ExecuteModifications(newModifications, fileDataStr)
+			atomic.AddInt64(&stats.TotalModifications, int64(count))
+			cmdLogger.Debug("Applied %d JSON modifications for command %q", count, command.Name)
+		}
+
+		count, ok := stats.ModificationsPerCommand.Load(command.Name)
+		if !ok {
+			count = 0
+		}
+		stats.ModificationsPerCommand.Store(command.Name, count.(int)+len(newModifications))
+	}
+
+	// Aggregate regex modifications and execute them
+	modifications := []utils.ReplaceCommand{}
+	numCommandsConsidered := 0
+	for _, command := range regexCommands {
+		cmdLogger := logger.Default
+		if cmdLog, ok := commandLoggers[command.Name]; ok {
+			cmdLogger = cmdLog
+		}
+
+		patterns := command.Regexes
+		if len(patterns) == 0 {
+			patterns = []string{command.Regex}
+		}
+		for idx, pattern := range patterns {
+			tmpCmd := command
+			tmpCmd.Regex = pattern
+			cmdLogger.Debug("Begin processing file with command %q (pattern %d/%d)", command.Name, idx+1, len(patterns))
+			numCommandsConsidered++
+			newModifications, err := processor.ProcessRegex(fileDataStr, tmpCmd, file)
+			if err != nil {
+				runOtherCommandsLogger.Error("Failed to process file with command %q: %v", command.Name, err)
+				continue
+			}
+			modifications = append(modifications, newModifications...)
+			count, ok := stats.ModificationsPerCommand.Load(command.Name)
+			if !ok {
+				count = 0
+			}
+			stats.ModificationsPerCommand.Store(command.Name, count.(int)+len(newModifications))
+
+			cmdLogger.Debug("Command %q generated %d modifications (pattern %d/%d)", command.Name, len(newModifications), idx+1, len(patterns))
+			cmdLogger.Trace("Modifications generated by command %q: %v", command.Name, newModifications)
+			if len(newModifications) == 0 {
+				cmdLogger.Debug("No modifications yielded by command %q (pattern %d/%d)", command.Name, idx+1, len(patterns))
+			}
+		}
+	}
+
+	runOtherCommandsLogger.Debug("Aggregated %d modifications from %d command-pattern runs", len(modifications), numCommandsConsidered)
+	runOtherCommandsLogger.Trace("All aggregated modifications: %v", modifications)
+
+	if len(modifications) == 0 {
+		runOtherCommandsLogger.Warning("No modifications found for file")
+		return fileDataStr, 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))
+
+	atomic.AddInt64(&stats.TotalModifications, int64(count))
+
+	runOtherCommandsLogger.Info("Executed %d modifications for file", count)
+	return fileDataStr, nil
+}
+
+func RunIsolateCommands(association utils.FileCommandAssociation, file string, fileDataStr string) (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 {
+		// Check if this isolate command should use JSON mode
+		if isolateCommand.JSON || *utils.JSON {
+			runIsolateCommandsLogger.Debug("Begin processing file with JSON isolate command %q", isolateCommand.Name)
+			modifications, err := processor.ProcessJSON(fileDataStr, isolateCommand, file)
+			if err != nil {
+				runIsolateCommandsLogger.Error("Failed to process file with JSON isolate command %q: %v", isolateCommand.Name, err)
+				continue
+			}
+
+			if len(modifications) == 0 {
+				runIsolateCommandsLogger.Debug("JSON isolate command %q produced no modifications", isolateCommand.Name)
+				continue
+			}
+			anythingDone = true
+
+			runIsolateCommandsLogger.Debug("Executing %d JSON isolate modifications for file", len(modifications))
+			runIsolateCommandsLogger.Trace("JSON isolate modifications: %v", modifications)
+			var count int
+			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 !anythingDone {
+		runIsolateCommandsLogger.Debug("No isolate modifications were made for file")
+		return fileDataStr, NothingToDo
+	}
+	return fileDataStr, nil
+}

processor/json.go

@@ -0,0 +1,216 @@
+package processor
+
+import (
+	"cook/utils"
+	"encoding/json"
+	"fmt"
+	"time"
+
+	logger "git.site.quack-lab.dev/dave/cylogger"
+	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)
+	}
+
+	// Marshal back to JSON
+	modifiedJSON, err := json.MarshalIndent(goData, "", "  ")
+	if err != nil {
+		processJsonLogger.Error("Failed to marshal modified data to JSON: %v", err)
+		return commands, fmt.Errorf("failed to marshal modified data to JSON: %v", err)
+	}
+
+	// Create replacement command for the entire file
+	// For JSON mode, we always replace the entire content
+	commands = append(commands, utils.ReplaceCommand{
+		From: 0,
+		To:   len(content),
+		With: string(modifiedJSON),
+	})
+
+	processJsonLogger.Debug("Total JSON processing time: %v", time.Since(startTime))
+	processJsonLogger.Debug("Generated %d total modifications", len(commands))
+	return commands, nil
+}
+
+// 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 +1,117 @@
+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": [{"id": 1, "value": 10}, {"id": 2, "value": 20}]}`,
+			luaExpression: `for i, item in ipairs(data.items) do data.items[i].value = item.value * 1.5 end; return true`,
+			expectedOutput: `{
+  "items": [
+    {
+      "id": 1,
+      "value": 15
+    },
+    {
+      "id": 2,
+      "value": 30
+    }
+  ]
+}`,
+			expectedMods: 1,
+		},
+		{
+			name:          "JSON nested object modification",
+			input:         `{"config": {"settings": {"enabled": false, "timeout": 30}}}`,
+			luaExpression: `data.config.settings.enabled = true; data.config.settings.timeout = 60; return true`,
+			expectedOutput: `{
+  "config": {
+    "settings": {
+      "enabled": true,
+      "timeout": 60
+    }
+  }
+}`,
+			expectedMods: 1,
+		},
+		{
+			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

@@ -2,154 +2,147 @@ package processor
 
 import (
 	"fmt"
+	"io"
+	"net/http"
+	"regexp"
 	"strings"
 
-	lua "github.com/yuin/gopher-lua"
+	"cook/utils"
 
-	"modify/logger"
+	logger "git.site.quack-lab.dev/dave/cylogger"
+	lua "github.com/yuin/gopher-lua"
 )
 
+// processorLogger is a scoped logger for the processor package.
+var processorLogger = logger.Default.WithPrefix("processor")
+
 // Maybe we make this an interface again for the shits and giggles
 // We will see, it could easily be...
 
+var globalVariables = map[string]interface{}{}
+
+func SetVariables(vars map[string]interface{}) {
+	for k, v := range vars {
+		globalVariables[k] = v
+	}
+}
+
 func NewLuaState() (*lua.LState, error) {
+	newLStateLogger := processorLogger.WithPrefix("NewLuaState")
+	newLStateLogger.Debug("Creating new Lua state")
 	L := lua.NewState()
 	// defer L.Close()
 
 	// Load math library
-	logger.Debug("Loading Lua math library")
+	newLStateLogger.Debug("Loading Lua math library")
 	L.Push(L.GetGlobal("require"))
 	L.Push(lua.LString("math"))
 	if err := L.PCall(1, 1, nil); err != nil {
-		logger.Error("Failed to load Lua math library: %v", err)
+		newLStateLogger.Error("Failed to load Lua math library: %v", err)
 		return nil, fmt.Errorf("error loading Lua math library: %v", err)
 	}
+	newLStateLogger.Debug("Lua math library loaded")
 
 	// Initialize helper functions
-	logger.Debug("Initializing Lua helper functions")
+	newLStateLogger.Debug("Initializing Lua helper functions")
 	if err := InitLuaHelpers(L); err != nil {
-		logger.Error("Failed to initialize Lua helper functions: %v", err)
+		newLStateLogger.Error("Failed to initialize Lua helper functions: %v", err)
 		return nil, err
 	}
+	newLStateLogger.Debug("Lua helper functions initialized")
 
+	// Inject global variables
+	if len(globalVariables) > 0 {
+		newLStateLogger.Debug("Injecting %d global variables into Lua state", len(globalVariables))
+		for k, v := range globalVariables {
+			switch val := v.(type) {
+			case int:
+				L.SetGlobal(k, lua.LNumber(float64(val)))
+			case int64:
+				L.SetGlobal(k, lua.LNumber(float64(val)))
+			case float32:
+				L.SetGlobal(k, lua.LNumber(float64(val)))
+			case float64:
+				L.SetGlobal(k, lua.LNumber(val))
+			case string:
+				L.SetGlobal(k, lua.LString(val))
+			case bool:
+				if val {
+					L.SetGlobal(k, lua.LTrue)
+				} else {
+					L.SetGlobal(k, lua.LFalse)
+				}
+			default:
+				// Fallback to string representation
+				L.SetGlobal(k, lua.LString(fmt.Sprintf("%v", val)))
+			}
+		}
+	}
+
+	newLStateLogger.Debug("New Lua state created successfully")
 	return L, nil
 }
 
-// func Process(filename string, pattern string, luaExpr string) (int, int, error) {
-// 	logger.Debug("Processing file %q with pattern %q", filename, pattern)
-//
-// 	// Read file content
-// 	cwd, err := os.Getwd()
-// 	if err != nil {
-// 		logger.Error("Failed to get current working directory: %v", err)
-// 		return 0, 0, fmt.Errorf("error getting current working directory: %v", err)
-// 	}
-//
-// 	fullPath := filepath.Join(cwd, filename)
-// 	logger.Trace("Reading file from: %s", fullPath)
-//
-// 	stat, err := os.Stat(fullPath)
-// 	if err != nil {
-// 		logger.Error("Failed to stat file %s: %v", fullPath, err)
-// 		return 0, 0, fmt.Errorf("error getting file info: %v", err)
-// 	}
-// 	logger.Debug("File size: %d bytes, modified: %s", stat.Size(), stat.ModTime().Format(time.RFC3339))
-//
-// 	content, err := os.ReadFile(fullPath)
-// 	if err != nil {
-// 		logger.Error("Failed to read file %s: %v", fullPath, err)
-// 		return 0, 0, fmt.Errorf("error reading file: %v", err)
-// 	}
-//
-// 	fileContent := string(content)
-// 	logger.Trace("File read successfully: %d bytes, hash: %x", len(content), md5sum(content))
-//
-// 	// Detect and log file type
-// 	fileType := detectFileType(filename, fileContent)
-// 	if fileType != "" {
-// 		logger.Debug("Detected file type: %s", fileType)
-// 	}
-//
-// 	// Process the content
-// 	logger.Debug("Starting content processing")
-// 	modifiedContent, modCount, matchCount, err := ProcessContent(fileContent, pattern, luaExpr)
-// 	if err != nil {
-// 		logger.Error("Processing error: %v", err)
-// 		return 0, 0, err
-// 	}
-//
-// 	logger.Debug("Processing results: %d matches, %d modifications", matchCount, modCount)
-//
-// 	// If we made modifications, save the file
-// 	if modCount > 0 {
-// 		// Calculate changes summary
-// 		changePercent := float64(len(modifiedContent)) / float64(len(fileContent)) * 100
-// 		logger.Info("File size change: %d → %d bytes (%.1f%%)",
-// 			len(fileContent), len(modifiedContent), changePercent)
-//
-// 		logger.Debug("Writing modified content to %s", fullPath)
-// 		err = os.WriteFile(fullPath, []byte(modifiedContent), 0644)
-// 		if err != nil {
-// 			logger.Error("Failed to write to file %s: %v", fullPath, err)
-// 			return 0, 0, fmt.Errorf("error writing file: %v", err)
-// 		}
-// 		logger.Debug("File written successfully, new hash: %x", md5sum([]byte(modifiedContent)))
-// 	} else if matchCount > 0 {
-// 		logger.Debug("No content modifications needed for %d matches", matchCount)
-// 	} else {
-// 		logger.Debug("No matches found in file")
-// 	}
-//
-// 	return modCount, matchCount, nil
-// }
-
 // FromLua converts a Lua table to a struct or map recursively
 func FromLua(L *lua.LState, luaValue lua.LValue) (interface{}, error) {
+	fromLuaLogger := processorLogger.WithPrefix("FromLua").WithField("luaType", luaValue.Type().String())
+	fromLuaLogger.Debug("Converting Lua value to Go interface")
 	switch v := luaValue.(type) {
-	// Well shit...
-	// Tables in lua are both maps and arrays
-	// As arrays they are ordered and as maps, obviously, not
-	// So when we parse them to a go map we fuck up the order for arrays
-	// We have to find a better way....
 	case *lua.LTable:
+		fromLuaLogger.Debug("Processing Lua table")
 		isArray, err := IsLuaTableArray(L, v)
 		if err != nil {
+			fromLuaLogger.Error("Failed to determine if Lua table is array: %v", err)
 			return nil, err
 		}
+		fromLuaLogger.Debug("Lua table is array: %t", isArray)
 		if isArray {
+			fromLuaLogger.Debug("Converting Lua table to Go array")
 			result := make([]interface{}, 0)
 			v.ForEach(func(key lua.LValue, value lua.LValue) {
 				converted, _ := FromLua(L, value)
 				result = append(result, converted)
 			})
+			fromLuaLogger.Trace("Converted Go array: %v", result)
 			return result, nil
 		} else {
+			fromLuaLogger.Debug("Converting Lua table to Go map")
 			result := make(map[string]interface{})
 			v.ForEach(func(key lua.LValue, value lua.LValue) {
 				converted, _ := FromLua(L, value)
 				result[key.String()] = converted
 			})
+			fromLuaLogger.Trace("Converted Go map: %v", result)
 			return result, nil
 		}
 	case lua.LString:
+		fromLuaLogger.Debug("Converting Lua string to Go string")
+		fromLuaLogger.Trace("Lua string: %q", string(v))
 		return string(v), nil
 	case lua.LBool:
+		fromLuaLogger.Debug("Converting Lua boolean to Go boolean")
+		fromLuaLogger.Trace("Lua boolean: %t", bool(v))
 		return bool(v), nil
 	case lua.LNumber:
+		fromLuaLogger.Debug("Converting Lua number to Go float64")
+		fromLuaLogger.Trace("Lua number: %f", float64(v))
 		return float64(v), nil
 	default:
+		fromLuaLogger.Debug("Unsupported Lua type, returning nil")
 		return nil, nil
 	}
 }
 
 func IsLuaTableArray(L *lua.LState, v *lua.LTable) (bool, error) {
-	logger.Trace("Checking if Lua table is an array")
+	isLuaTableArrayLogger := processorLogger.WithPrefix("IsLuaTableArray")
+	isLuaTableArrayLogger.Debug("Checking if Lua table is an array")
+	isLuaTableArrayLogger.Trace("Lua table input: %v", v)
 	L.SetGlobal("table_to_check", v)
 
 	// Use our predefined helper function from InitLuaHelpers
 	err := L.DoString(`is_array = isArray(table_to_check)`)
 	if err != nil {
-		logger.Error("Error determining if table is an array: %v", err)
+		isLuaTableArrayLogger.Error("Error determining if table is an array: %v", err)
 		return false, fmt.Errorf("error determining if table is array: %w", err)
 	}
 
@@ -157,13 +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
@@ -178,6 +173,7 @@ function ceil(x) return math.ceil(x) end
 function upper(s) return string.upper(s) end
 function lower(s) return string.lower(s) end
 function format(s, ...) return string.format(s, ...) end
+function trim(s) return string.gsub(s, "^%s*(.-)%s*$", "%1") end
 
 -- String split helper
 function strsplit(inputstr, sep)
@@ -243,25 +239,21 @@ 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))
+	initLuaHelpersLogger.Debug("Lua print and fetch functions bound to Go")
 	return nil
 }
 
-// LimitString truncates a string to maxLen and adds "..." if truncated
-func LimitString(s string, maxLen int) string {
-	s = strings.ReplaceAll(s, "\n", "\\n")
-	if len(s) <= maxLen {
-		return s
-	}
-	return s[:maxLen-3] + "..."
-}
-
 func PrependLuaAssignment(luaExpr string) string {
+	prependLuaAssignmentLogger := processorLogger.WithPrefix("PrependLuaAssignment").WithField("originalLuaExpr", luaExpr)
+	prependLuaAssignmentLogger.Debug("Prepending Lua assignment if necessary")
 	// Auto-prepend v1 for expressions starting with operators
 	if strings.HasPrefix(luaExpr, "*") ||
 		strings.HasPrefix(luaExpr, "/") ||
@@ -270,30 +262,32 @@ 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
@@ -301,11 +295,60 @@ 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)
@@ -319,8 +362,122 @@ 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"
+	var headers map[string]string = make(map[string]string)
+	var body string = ""
+
+	if L.GetTop() > 1 {
+		options := L.ToTable(2)
+		if options != nil {
+			fetchLogger.Debug("Processing fetch options")
+			// Get method
+			if methodVal := options.RawGetString("method"); methodVal != lua.LNil {
+				method = methodVal.String()
+				fetchLogger.Trace("Method from options: %q", method)
+			}
+
+			// Get headers
+			if headersVal := options.RawGetString("headers"); headersVal != lua.LNil {
+				if headersTable, ok := headersVal.(*lua.LTable); ok {
+					fetchLogger.Trace("Processing headers table")
+					headersTable.ForEach(func(key lua.LValue, value lua.LValue) {
+						headers[key.String()] = value.String()
+						fetchLogger.Trace("Header: %q = %q", key.String(), value.String())
+					})
+				}
+				fetchLogger.Trace("All headers: %v", headers)
+			}
+
+			// Get body
+			if bodyVal := options.RawGetString("body"); bodyVal != lua.LNil {
+				body = bodyVal.String()
+				fetchLogger.Trace("Body from options: %q", utils.LimitString(body, 100))
+			}
+		}
+	}
+	fetchLogger.Debug("Fetch request details: Method=%q, URL=%q, BodyLength=%d, Headers=%v", method, url, len(body), headers)
+
+	// Create HTTP request
+	req, err := http.NewRequest(method, url, strings.NewReader(body))
+	if err != nil {
+		fetchLogger.Error("Error creating HTTP request: %v", err)
+		L.Push(lua.LNil)
+		L.Push(lua.LString(fmt.Sprintf("Error creating request: %v", err)))
+		return 2
+	}
+
+	// Set headers
+	for key, value := range headers {
+		req.Header.Set(key, value)
+	}
+	fetchLogger.Debug("HTTP request created and headers set")
+	fetchLogger.Trace("HTTP Request: %+v", req)
+
+	// Make request
+	client := &http.Client{}
+	resp, err := client.Do(req)
+	if err != nil {
+		fetchLogger.Error("Error making HTTP request: %v", err)
+		L.Push(lua.LNil)
+		L.Push(lua.LString(fmt.Sprintf("Error making request: %v", err)))
+		return 2
+	}
+	defer func() {
+		fetchLogger.Debug("Closing HTTP response body")
+		resp.Body.Close()
+	}()
+	fetchLogger.Debug("HTTP request executed. Status Code: %d", resp.StatusCode)
+
+	// Read response body
+	bodyBytes, err := io.ReadAll(resp.Body)
+	if err != nil {
+		fetchLogger.Error("Error reading response body: %v", err)
+		L.Push(lua.LNil)
+		L.Push(lua.LString(fmt.Sprintf("Error reading response: %v", err)))
+		return 2
+	}
+	fetchLogger.Trace("Response body length: %d", len(bodyBytes))
+
+	// Create response table
+	responseTable := L.NewTable()
+	responseTable.RawSetString("status", lua.LNumber(resp.StatusCode))
+	responseTable.RawSetString("statusText", lua.LString(resp.Status))
+	responseTable.RawSetString("ok", lua.LBool(resp.StatusCode >= 200 && resp.StatusCode < 300))
+	responseTable.RawSetString("body", lua.LString(string(bodyBytes)))
+	fetchLogger.Debug("Created Lua response table")
+
+	// Set headers in response
+	headersTable := L.NewTable()
+	for key, values := range resp.Header {
+		headersTable.RawSetString(key, lua.LString(values[0]))
+		fetchLogger.Trace("Response header: %q = %q", key, values[0])
+	}
+	responseTable.RawSetString("headers", headersTable)
+	fetchLogger.Trace("Full response table: %v", responseTable)
+
+	L.Push(responseTable)
+	fetchLogger.Debug("Pushed response table to Lua stack")
+	return 1
+}

processor/regex.go

@@ -1,18 +1,20 @@
 package processor
 
 import (
+	"cook/utils"
 	"fmt"
 	"regexp"
 	"strconv"
 	"strings"
 	"time"
 
+	logger "git.site.quack-lab.dev/dave/cylogger"
 	lua "github.com/yuin/gopher-lua"
-
-	"modify/logger"
-	"modify/utils"
 )
 
+// regexLogger is a scoped logger for the processor/regex package.
+var regexLogger = logger.Default.WithPrefix("processor/regex")
+
 type CaptureGroup struct {
 	Name    string
 	Value   string
@@ -21,48 +23,62 @@ type CaptureGroup struct {
 }
 
 // ProcessContent applies regex replacement with Lua processing
-func ProcessRegex(content string, command utils.ModifyCommand) ([]utils.ReplaceCommand, error) {
+// The filename here exists ONLY so we can pass it to the lua environment
-	var commands []utils.ReplaceCommand
+// It's not used for anything else
-	logger.Trace("Processing regex: %q", command.Regex)
+func ProcessRegex(content string, command utils.ModifyCommand, filename string) ([]utils.ReplaceCommand, error) {
+	processRegexLogger := regexLogger.WithPrefix("ProcessRegex").WithField("commandName", command.Name).WithField("file", filename)
+	processRegexLogger.Debug("Starting regex processing for file")
+	processRegexLogger.Trace("Initial file content length: %d", len(content))
+	processRegexLogger.Trace("Command details: %+v", command)
 
+	var commands []utils.ReplaceCommand
 	// Start timing the regex processing
 	startTime := time.Now()
 
 	// We don't HAVE to do this multiple times for a pattern
 	// But it's quick enough for us to not care
 	pattern := resolveRegexPlaceholders(command.Regex)
-	logger.Debug("Compiling regex pattern: %s", pattern)
+	processRegexLogger.Debug("Resolved regex placeholders. Pattern: %s", pattern)
+
+	// I'm not too happy about having to trim regex, we could have meaningful whitespace or newlines
+	// But it's a compromise that allows us to use | in yaml
+	// Otherwise we would have to escape every god damn pair of quotation marks
+	// And a bunch of other shit
+	pattern = strings.TrimSpace(pattern)
+	processRegexLogger.Debug("Trimmed regex pattern: %s", pattern)
 
 	patternCompileStart := time.Now()
 	compiledPattern, err := regexp.Compile(pattern)
 	if err != nil {
-		logger.Error("Error compiling pattern: %v", err)
+		processRegexLogger.Error("Error compiling pattern %q: %v", pattern, err)
 		return commands, fmt.Errorf("error compiling pattern: %v", err)
 	}
-	logger.Debug("Compiled pattern successfully in %v: %s", time.Since(patternCompileStart), pattern)
+	processRegexLogger.Debug("Compiled pattern successfully in %v", 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
 	}
 
@@ -71,19 +87,21 @@ func ProcessRegex(content string, command utils.ModifyCommand) ([]utils.ReplaceC
 	// By going backwards we fuck up all the indices to the end of the file that we don't care about
 	// Because there either aren't any (last match) or they're already modified (subsequent matches)
 	for i, matchIndices := range indices {
-		logger.Debug("Processing match %d of %d", i+1, len(indices))
+		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))
 		// Hmm... Maybe we don't want to defer this..
 		// Maybe we want to close them every iteration
 		// We'll leave it as is for now
 		defer L.Close()
-		logger.Trace("Lua state created successfully for match %d", i+1)
+		matchLogger.Trace("Lua state created successfully for match %d", i+1)
 
 		// Why we're doing this whole song and dance of indices is to properly handle empty matches
 		// Plus it's a little cleaner to surgically replace our matches
@@ -92,20 +110,17 @@ func ProcessRegex(content string, command utils.ModifyCommand) ([]utils.ReplaceC
 		// So when we're cutting open the array we say 0:7 + modified + 7:end
 		// As if concatenating in the middle of the array
 		// Plus it supports lookarounds
-		match := content[matchIndices[0]:matchIndices[1]]
+		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
 		}
 
@@ -116,11 +131,11 @@ func ProcessRegex(content string, command utils.ModifyCommand) ([]utils.ReplaceC
 				validGroups++
 			}
 		}
-		logger.Debug("Found %d valid capture groups in match", validGroups)
+		matchLogger.Debug("Found %d valid capture groups in match", validGroups)
 
 		for _, index := range groups {
 			if index == -1 {
-				logger.Warning("Negative index encountered in match indices %v. This may indicate an issue with the regex pattern or an empty/optional capture group.", matchIndices)
+				matchLogger.Warning("Negative index encountered in match indices %v. This may indicate an issue with the regex pattern or an empty/optional capture group.", matchIndices)
 				continue
 			}
 		}
@@ -135,6 +150,7 @@ func ProcessRegex(content string, command utils.ModifyCommand) ([]utils.ReplaceC
 			start := groups[i*2]
 			end := groups[i*2+1]
 			if start == -1 || end == -1 {
+				matchLogger.Debug("Skipping empty or unmatched capture group #%d (name: %q)", i+1, name)
 				continue
 			}
 
@@ -147,71 +163,80 @@ func ProcessRegex(content string, command utils.ModifyCommand) ([]utils.ReplaceC
 
 			// Include name info in log if available
 			if name != "" {
-				logger.Trace("Capture group '%s': %q (pos %d-%d)", name, value, start, end)
+				matchLogger.Trace("Capture group '%s': %q (pos %d-%d)", name, value, start, end)
 			} else {
-				logger.Trace("Capture group #%d: %q (pos %d-%d)", i+1, value, start, end)
+				matchLogger.Trace("Capture group #%d: %q (pos %d-%d)", i+1, value, start, end)
 			}
 		}
 
+		// Use the DeduplicateGroups flag to control whether to deduplicate capture groups
+		if !command.NoDedup {
+			matchLogger.Debug("Deduplicating capture groups as specified in command settings")
 			captureGroups = deduplicateGroups(captureGroups)
+			matchLogger.Trace("Capture groups after deduplication: %v", captureGroups)
+		} else {
+			matchLogger.Debug("Skipping deduplication of capture groups (NoDedup is true)")
+		}
 
 		if err := toLua(L, captureGroups); err != nil {
-			logger.Error("Failed to set Lua variables: %v", err)
+			matchLogger.Error("Failed to set Lua variables for capture groups: %v", err)
 			continue
 		}
-		logger.Trace("Set %d capture groups as Lua variables", len(captureGroups))
+		matchLogger.Debug("Set %d capture groups as Lua variables", len(captureGroups))
+		matchLogger.Trace("Lua globals set for capture groups")
 
 		if err := L.DoString(luaExpr); err != nil {
-			logger.Error("Lua script execution failed: %v\nScript: %s\nCapture Groups: %+v",
+			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", capture.Value)
+					matchLogger.Debug("Capture group unchanged: %s", utils.LimitString(capture.Value, 50))
 					continue
 				}
 
 				// Log what changed with context
-				logger.Debug("Capture group %s scheduled for modification: %q → %q",
+				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
@@ -221,42 +246,57 @@ func ProcessRegex(content string, command utils.ModifyCommand) ([]utils.ReplaceC
 					To:   capture.Range[1],
 					With: capture.Updated,
 				})
+				matchLogger.Trace("Added replacement command: %+v", commands[len(commands)-1])
 			}
 		} else {
+			matchLogger.Debug("Using full replacement string from Lua: %q", utils.LimitString(replacement, 50))
 			commands = append(commands, utils.ReplaceCommand{
 				From: matchIndices[0],
 				To:   matchIndices[1],
 				With: replacement,
 			})
+			matchLogger.Trace("Added full replacement command: %+v", commands[len(commands)-1])
 		}
 	}
 
-	logger.Debug("Total regex processing time: %v", time.Since(startTime))
+	processRegexLogger.Debug("Total regex processing time: %v", time.Since(startTime))
+	processRegexLogger.Debug("Generated %d total modifications", len(commands))
 	return commands, nil
 }
 
 func deduplicateGroups(captureGroups []*CaptureGroup) []*CaptureGroup {
-	deduplicatedGroups := make([]*CaptureGroup, 0)
+	deduplicateGroupsLogger := regexLogger.WithPrefix("deduplicateGroups")
+	deduplicateGroupsLogger.Debug("Starting deduplication of capture groups")
+	deduplicateGroupsLogger.Trace("Input capture groups: %v", captureGroups)
+
+	// Preserve input order and drop any group that overlaps with an already accepted group
+	accepted := make([]*CaptureGroup, 0, len(captureGroups))
 	for _, group := range captureGroups {
+		groupLogger := deduplicateGroupsLogger.WithField("groupName", group.Name).WithField("groupRange", group.Range)
+		groupLogger.Debug("Processing capture group")
+
 		overlaps := false
-		logger.Debug("Checking capture group: %s with range %v", group.Name, group.Range)
+		for _, 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
@@ -265,105 +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
@@ -376,5 +494,6 @@ func estimatePatternComplexity(pattern string) int {
 	complexity += strings.Count(pattern, "\\1") * 3 // Backreferences
 	complexity += strings.Count(pattern, "{") * 2   // Counted repetition
 
+	estimateComplexityLogger.Debug("Estimated pattern complexity: %d", complexity)
 	return complexity
 }

processor/regex_test.go

@@ -2,9 +2,8 @@ package processor
 
 import (
 	"bytes"
-	"fmt"
+	"cook/utils"
 	"io"
-	"modify/utils"
 	"os"
 	"regexp"
 	"strings"
@@ -38,7 +37,7 @@ func ApiAdaptor(content string, regex string, lua string) (string, int, int, err
 		LogLevel: "TRACE",
 	}
 
-	commands, err := ProcessRegex(content, command)
+	commands, err := ProcessRegex(content, command, "test")
 	if err != nil {
 		return "", 0, 0, err
 	}

processor/test_helper.go

@@ -2,8 +2,9 @@ package processor
 
 import (
 	"io"
-	"modify/logger"
 	"os"
+
+	logger "git.site.quack-lab.dev/dave/cylogger"
 )
 
 func init() {
@@ -20,7 +21,7 @@ func init() {
 		if disableTestLogs {
 			// Create a new logger that writes to nowhere
 			silentLogger := logger.New(io.Discard, "", 0)
-			logger.DefaultLogger = silentLogger
+			logger.Default = silentLogger
 		}
 	}
 }

regression/regression_test.go

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

utils/db.go

@@ -0,0 +1,157 @@
+package utils
+
+import (
+	"path/filepath"
+	"time"
+
+	logger "git.site.quack-lab.dev/dave/cylogger"
+	"gorm.io/driver/sqlite"
+	"gorm.io/gorm"
+	gormlogger "gorm.io/gorm/logger"
+)
+
+// dbLogger is a scoped logger for the utils/db package.
+var dbLogger = logger.Default.WithPrefix("utils/db")
+
+type DB interface {
+	DB() *gorm.DB
+	Raw(sql string, args ...any) *gorm.DB
+	SaveFile(filePath string, fileData []byte) error
+	GetFile(filePath string) ([]byte, error)
+	GetAllFiles() ([]FileSnapshot, error)
+	RemoveAllFiles() error
+}
+
+type FileSnapshot struct {
+	Date     time.Time `gorm:"primaryKey"`
+	FilePath string    `gorm:"primaryKey"`
+	FileData []byte    `gorm:"type:blob"`
+}
+
+type DBWrapper struct {
+	db *gorm.DB
+}
+
+var globalDB *DBWrapper
+
+func GetDB() (DB, error) {
+	getDBLogger := dbLogger.WithPrefix("GetDB")
+	getDBLogger.Debug("Attempting to get database connection")
+	var err error
+
+	dbFile := filepath.Join("data.sqlite")
+	getDBLogger.Debug("Opening database file: %q", dbFile)
+	db, err := gorm.Open(sqlite.Open(dbFile), &gorm.Config{
+		// SkipDefaultTransaction: true,
+		PrepareStmt: true,
+		Logger:      gormlogger.Default.LogMode(gormlogger.Silent),
+	})
+	if err != nil {
+		getDBLogger.Error("Failed to open database: %v", err)
+		return nil, err
+	}
+	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")
+
+	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 {
+	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 {
+		saveFileLogger.Error("Error checking if file exists: %v", err)
+		return err
+	}
+	if exists {
+		saveFileLogger.Debug("File already exists, skipping save")
+		return nil
+	}
+	saveFileLogger.Debug("Creating new file snapshot in database")
+	err = db.db.Create(&FileSnapshot{
+		Date:     time.Now(),
+		FilePath: filePath,
+		FileData: fileData,
+	}).Error
+	if err != nil {
+		saveFileLogger.Error("Failed to create file snapshot: %v", err)
+	} else {
+		saveFileLogger.Debug("File saved successfully to database")
+	}
+	return err
+}
+
+func (db *DBWrapper) GetFile(filePath string) ([]byte, error) {
+	getFileLogger := dbLogger.WithPrefix("GetFile").WithField("filePath", filePath)
+	getFileLogger.Debug("Getting file from database")
+	var fileSnapshot FileSnapshot
+	err := db.db.Model(&FileSnapshot{}).Where("file_path = ?", filePath).First(&fileSnapshot).Error
+	if err != nil {
+		// 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
+	}
+	getFileLogger.Debug("File found in database")
+	getFileLogger.Trace("Retrieved file data length: %d", len(fileSnapshot.FileData))
+	return fileSnapshot.FileData, nil
+}
+
+func (db *DBWrapper) GetAllFiles() ([]FileSnapshot, error) {
+	getAllFilesLogger := dbLogger.WithPrefix("GetAllFiles")
+	getAllFilesLogger.Debug("Getting all files from database")
+	var fileSnapshots []FileSnapshot
+	err := db.db.Model(&FileSnapshot{}).Find(&fileSnapshots).Error
+	if err != nil {
+		getAllFilesLogger.Error("Failed to get all files from database: %v", err)
+		return nil, err
+	}
+	getAllFilesLogger.Debug("Found %d files in database", len(fileSnapshots))
+	getAllFilesLogger.Trace("File snapshots retrieved: %v", fileSnapshots)
+	return fileSnapshots, nil
+}
+
+func (db *DBWrapper) RemoveAllFiles() error {
+	removeAllFilesLogger := dbLogger.WithPrefix("RemoveAllFiles")
+	removeAllFilesLogger.Debug("Removing all files from database")
+	err := db.db.Exec("DELETE FROM file_snapshots").Error
+	if err != nil {
+		removeAllFilesLogger.Error("Failed to remove all files from database: %v", err)
+	} else {
+		removeAllFilesLogger.Debug("All files removed from database")
+	}
+	return err
+}

utils/file.go

@@ -0,0 +1,152 @@
+package utils
+
+import (
+	"os"
+	"path/filepath"
+	"strconv"
+	"strings"
+
+	logger "git.site.quack-lab.dev/dave/cylogger"
+)
+
+// fileLogger is a scoped logger for the utils/file package.
+var fileLogger = logger.Default.WithPrefix("utils/file")
+
+func CleanPath(path string) string {
+	cleanPathLogger := fileLogger.WithPrefix("CleanPath")
+	cleanPathLogger.Debug("Cleaning path: %q", path)
+	cleanPathLogger.Trace("Original path: %q", path)
+	path = filepath.Clean(path)
+	path = strings.ReplaceAll(path, "\\", "/")
+	cleanPathLogger.Trace("Cleaned path result: %q", path)
+	return path
+}
+
+func ToAbs(path string) string {
+	toAbsLogger := fileLogger.WithPrefix("ToAbs")
+	toAbsLogger.Debug("Converting path to absolute: %q", path)
+	toAbsLogger.Trace("Input path: %q", path)
+	if filepath.IsAbs(path) {
+		toAbsLogger.Debug("Path is already absolute, cleaning it.")
+		cleanedPath := CleanPath(path)
+		toAbsLogger.Trace("Already absolute path after cleaning: %q", cleanedPath)
+		return cleanedPath
+	}
+	cwd, err := os.Getwd()
+	if err != nil {
+		toAbsLogger.Error("Error getting current working directory: %v", err)
+		return CleanPath(path)
+	}
+	toAbsLogger.Trace("Current working directory: %q", cwd)
+	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 {
+	resetWhereNecessaryLogger := fileLogger.WithPrefix("ResetWhereNecessary")
+	resetWhereNecessaryLogger.Debug("Starting reset where necessary operation")
+	resetWhereNecessaryLogger.Trace("File-command associations input: %v", associations)
+	dirtyFiles := make(map[string]struct{})
+	for _, association := range associations {
+		resetWhereNecessaryLogger.Debug("Processing association for file: %q", association.File)
+		for _, command := range association.Commands {
+			resetWhereNecessaryLogger.Debug("Checking command %q for reset requirement", command.Name)
+			resetWhereNecessaryLogger.Trace("Command details: %v", command)
+			if command.Reset {
+				resetWhereNecessaryLogger.Debug("Command %q requires reset for file %q, marking as dirty", command.Name, association.File)
+				dirtyFiles[association.File] = struct{}{}
+			}
+		}
+		for _, command := range association.IsolateCommands {
+			resetWhereNecessaryLogger.Debug("Checking isolate command %q for reset requirement", command.Name)
+			resetWhereNecessaryLogger.Trace("Isolate command details: %v", command)
+			if command.Reset {
+				resetWhereNecessaryLogger.Debug("Isolate command %q requires reset for file %q, marking as dirty", command.Name, association.File)
+				dirtyFiles[association.File] = struct{}{}
+			}
+		}
+	}
+	resetWhereNecessaryLogger.Debug("Identified %d files that need to be reset", len(dirtyFiles))
+	resetWhereNecessaryLogger.Trace("Dirty files identified: %v", dirtyFiles)
+
+	for file := range dirtyFiles {
+		resetWhereNecessaryLogger.Debug("Resetting file %q", file)
+		fileData, err := db.GetFile(file)
+		if err != nil {
+			resetWhereNecessaryLogger.Warning("Failed to get original content for file %q from database: %v", file, err)
+			// Seed the snapshot from current disk content if missing, then use it as fallback
+			currentData, readErr := os.ReadFile(file)
+			if readErr != nil {
+				resetWhereNecessaryLogger.Warning("Additionally failed to read current file content for %q: %v", file, readErr)
+				continue
+			}
+			// Best-effort attempt to save baseline; ignore errors to avoid blocking reset
+			if saveErr := db.SaveFile(file, currentData); saveErr != nil {
+				resetWhereNecessaryLogger.Warning("Failed to seed baseline snapshot for %q: %v", file, saveErr)
+			}
+			fileData = currentData
+		}
+		resetWhereNecessaryLogger.Trace("Retrieved original file data length for %q: %d", file, len(fileData))
+		resetWhereNecessaryLogger.Debug("Writing original content back to file %q", file)
+		err = os.WriteFile(file, fileData, 0644)
+		if err != nil {
+			resetWhereNecessaryLogger.Warning("Failed to write original content back to file %q: %v", file, err)
+			continue
+		}
+		resetWhereNecessaryLogger.Debug("Successfully reset file %q", file)
+	}
+	resetWhereNecessaryLogger.Debug("Finished reset where necessary operation")
+	return nil
+}
+
+func ResetAllFiles(db DB) error {
+	resetAllFilesLogger := fileLogger.WithPrefix("ResetAllFiles")
+	resetAllFilesLogger.Debug("Starting reset all files operation")
+	fileSnapshots, err := db.GetAllFiles()
+	if err != nil {
+		resetAllFilesLogger.Error("Failed to get all file snapshots from database: %v", err)
+		return err
+	}
+	resetAllFilesLogger.Debug("Found %d files in database to reset", len(fileSnapshots))
+	resetAllFilesLogger.Trace("File snapshots retrieved: %v", fileSnapshots)
+
+	for _, fileSnapshot := range fileSnapshots {
+		resetAllFilesLogger.Debug("Resetting file %q", fileSnapshot.FilePath)
+		err = os.WriteFile(fileSnapshot.FilePath, fileSnapshot.FileData, 0644)
+		if err != nil {
+			resetAllFilesLogger.Warning("Failed to write file %q to disk: %v", fileSnapshot.FilePath, err)
+			continue
+		}
+		resetAllFilesLogger.Debug("File %q written to disk successfully", fileSnapshot.FilePath)
+	}
+	resetAllFilesLogger.Debug("Finished reset all files operation")
+	return nil
+}

utils/flags.go

@@ -2,15 +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 (
-	// Deprecated
-	GitFlag       = flag.Bool("git", false, "Use git to manage files")
-	// Deprecated
-	ResetFlag     = flag.Bool("reset", false, "Reset files to their original state")
-	LogLevel      = flag.String("loglevel", "INFO", "Set log level: ERROR, WARNING, INFO, DEBUG, TRACE")
-	Cookfile      = flag.String("cook", "**/cook.yml", "Path to cook config files, can be globbed")
 	ParallelFiles = flag.Int("P", 100, "Number of files to process in parallel")
-	Filter        = flag.String("filter", "", "Filter commands before running them")
+	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/git.go

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

utils/modifycommand.go

@@ -2,236 +2,374 @@ package utils
 
 import (
 	"fmt"
-	"modify/logger"
 	"os"
+	"path/filepath"
 	"strings"
 
+	logger "git.site.quack-lab.dev/dave/cylogger"
 	"github.com/bmatcuk/doublestar/v4"
 	"gopkg.in/yaml.v3"
 )
 
+// modifyCommandLogger is a scoped logger for the utils/modifycommand package.
+var modifyCommandLogger = logger.Default.WithPrefix("utils/modifycommand")
+
 type ModifyCommand struct {
-	Name     string   `yaml:"name"`
+	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"`
-	Git      bool     `yaml:"git"`
+	Files     []string               `yaml:"files,omitempty"`
-	Reset    bool     `yaml:"reset"`
+	Reset     bool                   `yaml:"reset,omitempty"`
-	LogLevel string   `yaml:"loglevel"`
+	LogLevel  string                 `yaml:"loglevel,omitempty"`
+	Isolate   bool                   `yaml:"isolate,omitempty"`
+	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
 }
 
 // Ehh.. Not much better... Guess this wasn't the big deal
 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 AssociateFilesWithCommands(files []string, commands []ModifyCommand) (map[string][]ModifyCommand, error) {
+func SplitPattern(pattern string) (string, string) {
-	associationCount := 0
+	splitPatternLogger := modifyCommandLogger.WithPrefix("SplitPattern").WithField("pattern", pattern)
-	fileCommands := make(map[string][]ModifyCommand)
+	splitPatternLogger.Debug("Splitting pattern")
-	for _, file := range files {
+	splitPatternLogger.Trace("Original pattern: %q", pattern)
-		for _, command := range commands {
+	static, pattern := doublestar.SplitPattern(pattern)
-			for _, glob := range command.Files {
+
-				matches, err := Matches(file, glob)
+	cwd, err := os.Getwd()
 	if err != nil {
-					logger.Trace("Failed to match glob %s with file %s: %v", glob, file, err)
+		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
+}
+
+type FileCommandAssociation struct {
+	File            string
+	IsolateCommands []ModifyCommand
+	Commands        []ModifyCommand
+}
+
+func AssociateFilesWithCommands(files []string, commands []ModifyCommand) (map[string]FileCommandAssociation, error) {
+	associateFilesLogger := modifyCommandLogger.WithPrefix("AssociateFilesWithCommands")
+	associateFilesLogger.Debug("Associating files with commands")
+	associateFilesLogger.Trace("Input files: %v", files)
+	associateFilesLogger.Trace("Input commands: %v", commands)
+	associationCount := 0
+	fileCommands := make(map[string]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)
+				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 {
+					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)
-					fileCommands[file] = append(fileCommands[file], command)
+					association := fileCommands[file]
+
+					if command.Isolate {
+						associateFilesLogger.Debug("Command %q is an isolate command, adding to isolate list", command.Name)
+						association.IsolateCommands = append(association.IsolateCommands, command)
+					} else {
+						associateFilesLogger.Debug("Command %q is a regular command, adding to regular list", command.Name)
+						association.Commands = append(association.Commands, command)
+					}
+					fileCommands[file] = association
 					associationCount++
+				} else {
+					associateFilesLogger.Trace("File %q did not match glob %q (pattern=%q, rel=%q)", file, glob, pattern, patternFile)
 				}
 			}
 		}
-		logger.Debug("Found %d commands for file %q", len(fileCommands[file]), file)
+		currentFileCommands := fileCommands[file]
-		if len(fileCommands[file]) == 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)
 	}
-	}
+	associateFilesLogger.Info("Completed association. Found %d total associations for %d files and %d commands", associationCount, len(files), len(commands))
-	logger.Info("Found %d associations between %d files and %d commands", associationCount, len(files), len(commands))
 	return fileCommands, nil
 }
 
 func AggregateGlobs(commands []ModifyCommand) map[string]struct{} {
-	logger.Info("Aggregating globs for %d commands", len(commands))
+	aggregateGlobsLogger := modifyCommandLogger.WithPrefix("AggregateGlobs")
+	aggregateGlobsLogger.Debug("Aggregating glob patterns from commands")
+	aggregateGlobsLogger.Trace("Input commands for aggregation: %v", commands)
 	globs := make(map[string]struct{})
 	for _, command := range commands {
+		aggregateGlobsLogger.Debug("Processing command %q for glob patterns", command.Name)
 		for _, glob := range command.Files {
-			globs[glob] = struct{}{}
+			resolvedGlob := strings.Replace(glob, "~", os.Getenv("HOME"), 1)
+			resolvedGlob = strings.ReplaceAll(resolvedGlob, "\\", "/")
+			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)
-		matches, _ := doublestar.Glob(os.DirFS(cwd), pattern)
+		static, pattern := SplitPattern(pattern)
-		logger.Debug("Found %d matches for pattern %s", len(matches), pattern)
+		matches, err := doublestar.Glob(os.DirFS(static), 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", *Cookfile)
+	for _, arg := range args {
-	newcommands, err := LoadCommandsFromCookFiles(*Cookfile)
+		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)
-	commands = append(commands, newcommands...)
+		for _, cmd := range newCommands {
-	logger.Info("Now total commands: %d", len(commands))
+			if cmd.Disabled {
-
+				loadCommandsLogger.Debug("Skipping disabled command: %q", cmd.Name)
-	logger.Info("Loading commands from arguments: %v", args)
+				continue
-	newcommands, err = LoadCommandFromArgs(args)
+			}
-	if err != nil {
+			commands = append(commands, cmd)
-		if len(commands) == 0 {
+			loadCommandsLogger.Trace("Added command %q. Current total commands: %d", cmd.Name, len(commands))
-			return nil, fmt.Errorf("failed to load commands from args: %w", err)
 		}
-		logger.Warning("Failed to load commands from args: %v", err)
 	}
-	logger.Info("Successfully loaded %d commands from args", len(newcommands))
-	commands = append(commands, newcommands...)
-	logger.Info("Now total commands: %d", len(commands))
 
+	loadCommandsLogger.Info("Finished loading commands. Total %d commands loaded", len(commands))
 	return commands, nil
 }
 
-func LoadCommandFromArgs(args []string) ([]ModifyCommand, error) {
+func LoadCommandsFromCookFiles(pattern string) ([]ModifyCommand, error) {
-	// Cannot reset without git, right?
+	loadCookFilesLogger := modifyCommandLogger.WithPrefix("LoadCommandsFromCookFiles").WithField("pattern", pattern)
-	if *ResetFlag {
+	loadCookFilesLogger.Debug("Loading commands from cook files based on pattern")
-		*GitFlag = true
+	loadCookFilesLogger.Trace("Input pattern: %q", pattern)
-	}
+	static, pattern := SplitPattern(pattern)
-
-	if len(args) < 3 {
-		return nil, fmt.Errorf("at least %d arguments are required", 3)
-	}
-
-	command := ModifyCommand{
-		Regex:    args[0],
-		Lua:      args[1],
-		Files:    args[2:],
-		Git:      *GitFlag,
-		Reset:    *ResetFlag,
-		LogLevel: *LogLevel,
-	}
-
-	if err := command.Validate(); err != nil {
-		return nil, fmt.Errorf("invalid command: %w", err)
-	}
-
-	return []ModifyCommand{command}, nil
-}
-
-func LoadCommandsFromCookFiles(s string) ([]ModifyCommand, error) {
-	cwd, err := os.Getwd()
-	if err != nil {
-		return nil, fmt.Errorf("failed to get current working directory: %w", err)
-	}
-
 	commands := []ModifyCommand{}
-	cookFiles, err := doublestar.Glob(os.DirFS(cwd), *Cookfile)
+	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, "\\", "/")
+		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/modifycommand_test.go

@@ -158,21 +158,24 @@ func TestAssociateFilesWithCommands(t *testing.T) {
 
 	// The associations expected depends on the implementation
 	// Let's check the actual associations and verify they make sense
-	for file, cmds := range associations {
+	for file, assoc := range associations {
-		t.Logf("File %s is associated with %d commands", file, len(cmds))
+		t.Logf("File %s is associated with %d commands and %d isolate commands", file, len(assoc.Commands), len(assoc.IsolateCommands))
-		for i, cmd := range cmds {
+		for i, cmd := range assoc.Commands {
 			t.Logf("  Command %d: Pattern=%s, Files=%v", i, cmd.Regex, cmd.Files)
 		}
+		for i, cmd := range assoc.IsolateCommands {
+			t.Logf("  Isolate Command %d: Pattern=%s, Files=%v", i, cmd.Regex, cmd.Files)
+		}
 
 		// Specific validation based on our file types
 		switch file {
 		case "file1.xml":
-			if len(cmds) < 1 {
+			if len(assoc.Commands) < 1 {
-				t.Errorf("Expected at least 1 command for file1.xml, got %d", len(cmds))
+				t.Errorf("Expected at least 1 command for file1.xml, got %d", len(assoc.Commands))
 			}
 			// Verify at least one command with *.xml pattern
 			hasXmlGlob := false
-			for _, cmd := range cmds {
+			for _, cmd := range assoc.Commands {
 				for _, glob := range cmd.Files {
 					if glob == "*.xml" {
 						hasXmlGlob = true
@@ -187,12 +190,12 @@ func TestAssociateFilesWithCommands(t *testing.T) {
 				t.Errorf("Expected command with *.xml glob for file1.xml")
 			}
 		case "file2.txt":
-			if len(cmds) < 1 {
+			if len(assoc.Commands) < 1 {
-				t.Errorf("Expected at least 1 command for file2.txt, got %d", len(cmds))
+				t.Errorf("Expected at least 1 command for file2.txt, got %d", len(assoc.Commands))
 			}
 			// Verify at least one command with *.txt pattern
 			hasTxtGlob := false
-			for _, cmd := range cmds {
+			for _, cmd := range assoc.Commands {
 				for _, glob := range cmd.Files {
 					if glob == "*.txt" {
 						hasTxtGlob = true
@@ -207,12 +210,12 @@ func TestAssociateFilesWithCommands(t *testing.T) {
 				t.Errorf("Expected command with *.txt glob for file2.txt")
 			}
 		case "subdir/file3.xml":
-			if len(cmds) < 1 {
+			if len(assoc.Commands) < 1 {
-				t.Errorf("Expected at least 1 command for subdir/file3.xml, got %d", len(cmds))
+				t.Errorf("Expected at least 1 command for subdir/file3.xml, got %d", len(assoc.Commands))
 			}
 			// Should match both *.xml and subdir/* patterns
 			matches := 0
-			for _, cmd := range cmds {
+			for _, cmd := range assoc.Commands {
 				for _, glob := range cmd.Files {
 					if glob == "*.xml" || glob == "subdir/*" {
 						matches++
@@ -266,137 +269,15 @@ func TestAggregateGlobs(t *testing.T) {
 	}
 }
 
-func TestLoadCommandFromArgs(t *testing.T) {
-	// Save original flags
-	origGitFlag := *GitFlag
-	origResetFlag := *ResetFlag
-	origLogLevel := *LogLevel
-
-	// Restore original flags after test
-	defer func() {
-		*GitFlag = origGitFlag
-		*ResetFlag = origResetFlag
-		*LogLevel = origLogLevel
-	}()
-
-	// Test cases
-	tests := []struct {
-		name        string
-		args        []string
-		gitFlag     bool
-		resetFlag   bool
-		logLevel    string
-		shouldError bool
-	}{
-		{
-			name:        "Valid command",
-			args:        []string{"pattern", "expr", "file1", "file2"},
-			gitFlag:     false,
-			resetFlag:   false,
-			logLevel:    "INFO",
-			shouldError: false,
-		},
-		{
-			name:        "Not enough args",
-			args:        []string{"pattern", "expr"},
-			gitFlag:     false,
-			resetFlag:   false,
-			logLevel:    "INFO",
-			shouldError: true,
-		},
-		{
-			name:        "With git flag",
-			args:        []string{"pattern", "expr", "file1"},
-			gitFlag:     true,
-			resetFlag:   false,
-			logLevel:    "INFO",
-			shouldError: false,
-		},
-		{
-			name:        "With reset flag (forces git flag)",
-			args:        []string{"pattern", "expr", "file1"},
-			gitFlag:     false,
-			resetFlag:   true,
-			logLevel:    "INFO",
-			shouldError: false,
-		},
-		{
-			name:        "With custom log level",
-			args:        []string{"pattern", "expr", "file1"},
-			gitFlag:     false,
-			resetFlag:   false,
-			logLevel:    "DEBUG",
-			shouldError: false,
-		},
-	}
-
-	for _, tc := range tests {
-		t.Run(tc.name, func(t *testing.T) {
-			// Set flags for this test case
-			*GitFlag = tc.gitFlag
-			*ResetFlag = tc.resetFlag
-			*LogLevel = tc.logLevel
-
-			commands, err := LoadCommandFromArgs(tc.args)
-
-			if tc.shouldError {
-				if err == nil {
-					t.Errorf("Expected an error but got none")
-				}
-				return
-			}
-
-			if err != nil {
-				t.Errorf("Unexpected error: %v", err)
-				return
-			}
-
-			if len(commands) != 1 {
-				t.Errorf("Expected 1 command, got %d", len(commands))
-				return
-			}
-
-			cmd := commands[0]
-
-			// Check command properties
-			if cmd.Regex != tc.args[0] {
-				t.Errorf("Expected pattern %q, got %q", tc.args[0], cmd.Regex)
-			}
-
-			if cmd.Lua != tc.args[1] {
-				t.Errorf("Expected LuaExpr %q, got %q", tc.args[1], cmd.Lua)
-			}
-
-			if len(cmd.Files) != len(tc.args)-2 {
-				t.Errorf("Expected %d files, got %d", len(tc.args)-2, len(cmd.Files))
-			}
-
-			// When reset is true, git should be true regardless of what was set
-			expectedGit := tc.gitFlag || tc.resetFlag
-			if cmd.Git != expectedGit {
-				t.Errorf("Expected Git flag %v, got %v", expectedGit, cmd.Git)
-			}
-
-			if cmd.Reset != tc.resetFlag {
-				t.Errorf("Expected Reset flag %v, got %v", tc.resetFlag, cmd.Reset)
-			}
-
-			if cmd.LogLevel != tc.logLevel {
-				t.Errorf("Expected LogLevel %q, got %q", tc.logLevel, cmd.LogLevel)
-			}
-		})
-	}
-}
-
 // Successfully unmarshal valid YAML data into ModifyCommand slice
 func TestLoadCommandsFromCookFileSuccess(t *testing.T) {
 	// Arrange
 	yamlData := []byte(`
 - name: command1
-  pattern: "*.txt"
+  regex: "*.txt"
   lua: replace
 - name: command2
-  pattern: "*.go"
+  regex: "*.go"
   lua: delete
 `)
 
@@ -420,11 +301,11 @@ func TestLoadCommandsFromCookFileWithComments(t *testing.T) {
 	yamlData := []byte(`
     # This is a comment
     - name: command1
-      pattern: "*.txt"
+      regex: "*.txt"
       lua: replace
     # Another comment
     - name: command2
-      pattern: "*.go"
+      regex: "*.go"
       lua: delete
     `)
 
@@ -445,7 +326,7 @@ func TestLoadCommandsFromCookFileWithComments(t *testing.T) {
 // Handle different YAML formatting styles (flow vs block)
 func TestLoadCommandsFromCookFileWithFlowStyle(t *testing.T) {
 	// Arrange
-	yamlData := []byte(`[ { name: command1, pattern: "*.txt", lua: replace }, { name: command2, pattern: "*.go", lua: delete } ]`)
+	yamlData := []byte(`[ { name: command1, regex: "*.txt", lua: replace }, { name: command2, regex: "*.go", lua: delete } ]`)
 
 	// Act
 	commands, err := LoadCommandsFromCookFile(yamlData)
@@ -496,13 +377,13 @@ func TestLoadCommandsFromCookFileWithMultipleEntries(t *testing.T) {
 	// Arrange
 	yamlData := []byte(`
 - name: command1
-  pattern: "*.txt"
+  regex: "*.txt"
   lua: replace
 - name: command2
-  pattern: "*.go"
+  regex: "*.go"
   lua: delete
 - name: command3
-  pattern: "*.md"
+  regex: "*.md"
   lua: append
 `)
 
@@ -553,155 +434,6 @@ func TestLoadCommandsFromCookFileLegitExample(t *testing.T) {
 	assert.Equal(t, "crewlayabout", commands[0].Name)
 }
 
-// Valid command with minimum 3 arguments returns a ModifyCommand slice with correct values
-func TestLoadCommandFromArgsWithValidArguments(t *testing.T) {
-	// Setup
-	oldGitFlag := GitFlag
-	oldResetFlag := ResetFlag
-	oldLogLevel := LogLevel
-
-	gitValue := true
-	resetValue := false
-	logLevelValue := "info"
-
-	GitFlag = &gitValue
-	ResetFlag = &resetValue
-	LogLevel = &logLevelValue
-
-	defer func() {
-		GitFlag = oldGitFlag
-		ResetFlag = oldResetFlag
-		LogLevel = oldLogLevel
-	}()
-
-	args := []string{"*.go", "return x", "file1.go", "file2.go"}
-
-	// Execute
-	commands, err := LoadCommandFromArgs(args)
-
-	// Assert
-	assert.NoError(t, err)
-	assert.Len(t, commands, 1)
-	assert.Equal(t, "*.go", commands[0].Regex)
-	assert.Equal(t, "return x", commands[0].Lua)
-	assert.Equal(t, []string{"file1.go", "file2.go"}, commands[0].Files)
-	assert.Equal(t, true, commands[0].Git)
-	assert.Equal(t, false, commands[0].Reset)
-	assert.Equal(t, "info", commands[0].LogLevel)
-}
-
-// Less than 3 arguments returns an error with appropriate message
-func TestLoadCommandFromArgsWithInsufficientArguments(t *testing.T) {
-	// Setup
-	oldGitFlag := GitFlag
-	oldResetFlag := ResetFlag
-	oldLogLevel := LogLevel
-
-	gitValue := false
-	resetValue := false
-	logLevelValue := "info"
-
-	GitFlag = &gitValue
-	ResetFlag = &resetValue
-	LogLevel = &logLevelValue
-
-	defer func() {
-		GitFlag = oldGitFlag
-		ResetFlag = oldResetFlag
-		LogLevel = oldLogLevel
-	}()
-
-	testCases := []struct {
-		name string
-		args []string
-	}{
-		{"empty args", []string{}},
-		{"one arg", []string{"*.go"}},
-		{"two args", []string{"*.go", "return x"}},
-	}
-
-	for _, tc := range testCases {
-		t.Run(tc.name, func(t *testing.T) {
-			// Execute
-			commands, err := LoadCommandFromArgs(tc.args)
-
-			// Assert
-			assert.Error(t, err)
-			assert.Nil(t, commands)
-			assert.Contains(t, err.Error(), "at least 3 arguments are required")
-		})
-	}
-}
-
-// Pattern, Lua, and Files fields are correctly populated from args
-func TestLoadCommandFromArgsPopulatesFieldsCorrectly(t *testing.T) {
-	// Setup
-	oldGitFlag := GitFlag
-	oldResetFlag := ResetFlag
-	oldLogLevel := LogLevel
-
-	gitValue := false
-	resetValue := false
-	logLevelValue := "debug"
-
-	GitFlag = &gitValue
-	ResetFlag = &resetValue
-	LogLevel = &logLevelValue
-
-	defer func() {
-		GitFlag = oldGitFlag
-		ResetFlag = oldResetFlag
-		LogLevel = oldLogLevel
-	}()
-
-	args := []string{"*.txt", "print('Hello')", "file1.txt", "file2.txt"}
-
-	// Execute
-	commands, err := LoadCommandFromArgs(args)
-
-	// Assert
-	assert.NoError(t, err)
-	assert.Len(t, commands, 1)
-	assert.Equal(t, "*.txt", commands[0].Regex)
-	assert.Equal(t, "print('Hello')", commands[0].Lua)
-	assert.Equal(t, []string{"file1.txt", "file2.txt"}, commands[0].Files)
-	assert.Equal(t, false, commands[0].Git)
-	assert.Equal(t, false, commands[0].Reset)
-	assert.Equal(t, "debug", commands[0].LogLevel)
-}
-
-// Git flag is set to true when ResetFlag is true
-func TestLoadCommandFromArgsSetsGitFlagWhenResetFlagIsTrue(t *testing.T) {
-	// Setup
-	oldGitFlag := GitFlag
-	oldResetFlag := ResetFlag
-	oldLogLevel := LogLevel
-
-	gitValue := false
-	resetValue := true
-	logLevelValue := "info"
-
-	GitFlag = &gitValue
-	ResetFlag = &resetValue
-	LogLevel = &logLevelValue
-
-	defer func() {
-		GitFlag = oldGitFlag
-		ResetFlag = oldResetFlag
-		LogLevel = oldLogLevel
-	}()
-
-	args := []string{"*.go", "return x", "file1.go", "file2.go"}
-
-	// Execute
-	commands, err := LoadCommandFromArgs(args)
-
-	// Assert
-	assert.NoError(t, err)
-	assert.Len(t, commands, 1)
-	assert.Equal(t, true, commands[0].Git)
-}
-
 // TODO: Figure out how to mock shit
 // Can't be asked doing that right now...
 // Successfully loads commands from multiple YAML files in the current directory

utils/replacecommand.go

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