Convert \n to \r?\n because of windows thank you windows :)

It was adding backslashes and shit

go.mod

@@ -15,12 +15,15 @@ require (
 	github.com/BurntSushi/toml v1.5.0 // indirect
 	github.com/davecgh/go-spew v1.1.1 // indirect
 	github.com/hexops/valast v1.5.0 // indirect
+	github.com/inconshreveable/mousetrap v1.1.0 // indirect
 	github.com/jinzhu/inflection v1.0.0 // indirect
 	github.com/jinzhu/now v1.1.5 // indirect
 	github.com/kr/pretty v0.3.1 // indirect
 	github.com/mattn/go-sqlite3 v1.14.22 // indirect
 	github.com/pmezard/go-difflib v1.0.0 // indirect
 	github.com/rogpeppe/go-internal v1.14.1 // indirect
+	github.com/spf13/cobra v1.10.1 // indirect
+	github.com/spf13/pflag v1.0.9 // indirect
 	github.com/tidwall/match v1.1.1 // indirect
 	github.com/tidwall/pretty v1.2.0 // indirect
 	golang.org/x/mod v0.21.0 // indirect

go.sum

@@ -4,6 +4,7 @@ github.com/BurntSushi/toml v1.5.0 h1:W5quZX/G/csjUnuI8SUYlsHs9M38FC7znL0lIO+DvMg
 github.com/BurntSushi/toml v1.5.0/go.mod h1:ukJfTF/6rtPPRCnwkur4qwRxa8vTRFBF0uk2lLoLwho=
 github.com/bmatcuk/doublestar/v4 v4.8.1 h1:54Bopc5c2cAvhLRAzqOGCYHYyhcDHsFF4wWIR5wKP38=
 github.com/bmatcuk/doublestar/v4 v4.8.1/go.mod h1:xBQ8jztBU6kakFMg+8WGxn0c6z1fTSPVIjEY1Wr7jzc=
+github.com/cpuguy83/go-md2man/v2 v2.0.6/go.mod h1:oOW0eioCTA6cOiMLiUPZOpcVxMig6NIQQ7OS05n1F4g=
 github.com/creack/pty v1.1.9/go.mod h1:oKZEueFk5CKHvIhNR5MUki03XCEU+Q6VDXinZuGJ33E=
 github.com/davecgh/go-spew v1.1.1 h1:vj9j/u1bqnvCEfJOwUhtlOARqs3+rkHYY13jYWTU97c=
 github.com/davecgh/go-spew v1.1.1/go.mod h1:J7Y8YcW2NihsgmVo/mv3lAwl/skON4iLHjSsI+c5H38=
@@ -17,6 +18,8 @@ github.com/hexops/gotextdiff v1.0.3 h1:gitA9+qJrrTCsiCl7+kh75nPqQt1cx4ZkudSTLoUq
 github.com/hexops/gotextdiff v1.0.3/go.mod h1:pSWU5MAI3yDq+fZBTazCSJysOMbxWL1BSow5/V2vxeg=
 github.com/hexops/valast v1.5.0 h1:FBTuvVi0wjTngtXJRZXMbkN/Dn6DgsUsBwch2DUJU8Y=
 github.com/hexops/valast v1.5.0/go.mod h1:Jcy1pNH7LNraVaAZDLyv21hHg2WBv9Nf9FL6fGxU7o4=
+github.com/inconshreveable/mousetrap v1.1.0 h1:wN+x4NVGpMsO7ErUn/mUI3vEoE6Jt13X2s0bqwp9tc8=
+github.com/inconshreveable/mousetrap v1.1.0/go.mod h1:vpF70FUmC8bwa3OWnCshd2FqLfsEA9PFc4w1p2J65bw=
 github.com/jinzhu/inflection v1.0.0 h1:K317FqzuhWc8YvSVlFMCCUb36O/S9MCKRDI7QkRKD/E=
 github.com/jinzhu/inflection v1.0.0/go.mod h1:h+uFLlag+Qp1Va5pdKtLDYj+kHp5pxUVkryuEj+Srlc=
 github.com/jinzhu/now v1.1.5 h1:/o9tlHleP7gOFmsnYNz3RGnqzefHA47wQpKrrdTIwXQ=
@@ -36,6 +39,11 @@ github.com/pmezard/go-difflib v1.0.0/go.mod h1:iKH77koFhYxTK1pcRnkKkqfTogsbg7gZN
 github.com/rogpeppe/go-internal v1.9.0/go.mod h1:WtVeX8xhTBvf0smdhujwtBcq4Qrzq/fJaraNFVN+nFs=
 github.com/rogpeppe/go-internal v1.14.1 h1:UQB4HGPB6osV0SQTLymcB4TgvyWu6ZyliaW0tI/otEQ=
 github.com/rogpeppe/go-internal v1.14.1/go.mod h1:MaRKkUm5W0goXpeCfT7UZI6fk/L7L7so1lCWt35ZSgc=
+github.com/russross/blackfriday/v2 v2.1.0/go.mod h1:+Rmxgy9KzJVeS9/2gXHxylqXiyQDYRxCVz55jmeOWTM=
+github.com/spf13/cobra v1.10.1 h1:lJeBwCfmrnXthfAupyUTzJ/J4Nc1RsHC/mSRU2dll/s=
+github.com/spf13/cobra v1.10.1/go.mod h1:7SmJGaTHFVBY0jW4NXGluQoLvhqFQM+6XSKD+P4XaB0=
+github.com/spf13/pflag v1.0.9 h1:9exaQaMOCwffKiiiYk6/BndUBv+iRViNW+4lEMi0PvY=
+github.com/spf13/pflag v1.0.9/go.mod h1:McXfInJRrz4CZXVZOBLb0bTZqETkiAhM9Iw0y3An2Bg=
 github.com/stretchr/testify v1.10.0 h1:Xv5erBjTwe/5IxqUQTdXv5kgmIvbHo3QQyRwhJsOfJA=
 github.com/stretchr/testify v1.10.0/go.mod h1:r2ic/lqez/lEtzL7wO/rwa5dbSLXVDPFyf8C91i36aY=
 github.com/tidwall/gjson v1.18.0 h1:FIDeeyB800efLX89e5a8Y0BNH+LOngJyGrIWxG2FKQY=

main.go

@@ -3,8 +3,6 @@ package main
 import (
 	_ "embed"
 	"errors"
-	"flag"
-	"fmt"
 	"os"
 	"sort"
 	"sync"
@@ -14,6 +12,7 @@ import (
 	"cook/processor"
 	"cook/utils"
 
+	"github.com/spf13/cobra"
 	logger "git.site.quack-lab.dev/dave/cylogger"
 )
 
@@ -37,52 +36,114 @@ var (
 	}
 )
 
-func main() {
+// rootCmd represents the base command when called without any subcommands
-	flag.Usage = func() {
+var rootCmd *cobra.Command
-		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, "  -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, "  -conv\n")
-		fmt.Fprintf(os.Stderr, "        Convert YAML files to TOML format\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, "  JSON mode:\n")
-		fmt.Fprintf(os.Stderr, "    %s -json data.json\n", os.Args[0])
-		fmt.Fprintf(os.Stderr, "  YAML to TOML conversion:\n")
-		fmt.Fprintf(os.Stderr, "    %s -conv *.yml\n", os.Args[0])
-		fmt.Fprintf(os.Stderr, "    %s -conv **/*.yaml\n", os.Args[0])
-		fmt.Fprintf(os.Stderr, "\nNote: v1, v2, etc. are used to refer to capture groups as numbers.\n")
-		fmt.Fprintf(os.Stderr, "      s1, s2, etc. are used to refer to capture groups as strings.\n")
-		fmt.Fprintf(os.Stderr, "      Helper functions: num(str) converts string to number, str(num) converts number to string\n")
-		fmt.Fprintf(os.Stderr, "      is_number(str) checks if a string is numeric\n")
-		fmt.Fprintf(os.Stderr, "      If expression starts with an operator like *, /, +, -, =, etc., v1 is automatically prepended\n")
-		fmt.Fprintf(os.Stderr, "      You can use any valid Lua code, including if statements, loops, etc.\n")
-		fmt.Fprintf(os.Stderr, "      Glob patterns are supported for file selection (*.xml, data/**.xml, etc.)\n")
-		fmt.Fprintf(os.Stderr, "\nLua Functions Available:\n")
-		fmt.Fprintf(os.Stderr, "%s\n", processor.GetLuaFunctionsHelp())
-	}
-	// TODO: Fix bed shitting when doing *.yml in barotrauma directory
-	flag.Parse()
-	args := flag.Args()
 
+func init() {
+	rootCmd = &cobra.Command{
+		Use:   "modifier [options] <pattern> <lua_expression> <...files_or_globs>",
+		Short: "A powerful file modification tool with Lua scripting",
+		Long: `Modifier is a powerful file processing tool that supports regex patterns,
+JSON manipulation, and YAML to TOML conversion with Lua scripting capabilities.
+
+Features:
+- Regex-based pattern matching and replacement
+- JSON file processing with query support
+- YAML to TOML conversion
+- Lua scripting for complex transformations
+- Parallel file processing
+- Command filtering and organization`,
+		PersistentPreRun: func(cmd *cobra.Command, args []string) {
+			CreateExampleConfig()
 			logger.InitFlag()
 			mainLogger.Info("Initializing with log level: %s", logger.GetLevel().String())
 			mainLogger.Trace("Full argv: %v", os.Args)
-
+		},
-	if flag.NArg() == 0 {
+		Run: func(cmd *cobra.Command, args []string) {
-		flag.Usage()
+			if len(args) == 0 {
+				cmd.Usage()
 				return
 			}
+			runModifier(args, cmd)
+		},
+	}
+
+	// Global flags
+	rootCmd.PersistentFlags().StringP("loglevel", "l", "INFO", "Set logging level: ERROR, WARNING, INFO, DEBUG, TRACE")
+
+	// Local flags
+	rootCmd.Flags().IntP("parallel", "P", 100, "Number of files to process in parallel")
+	rootCmd.Flags().StringP("filter", "f", "", "Filter commands before running them")
+	rootCmd.Flags().Bool("json", false, "Enable JSON mode for processing JSON files")
+	rootCmd.Flags().BoolP("conv", "c", false, "Convert YAML files to TOML format")
+
+	// Set up examples in the help text
+	rootCmd.SetUsageTemplate(`Usage:{{if .Runnable}}
+  {{.UseLine}}{{end}}{{if .HasAvailableSubCommands}}
+  {{.CommandPath}} [command]{{end}} {{if gt (len .Aliases) 0}}
+
+Aliases:
+  {{.NameAndAliases}}{{end}}{{if .HasExample}}
+
+Examples:
+{{.Example}}{{end}}{{if .HasAvailableSubCommands}}
+
+Available Commands:{{range .Commands}}{{if (or .IsAvailableCommand (eq .Name "help"))}}
+  {{rpad .Name .NamePadding }} {{.Short}}{{end}}{{end}}{{end}}{{if .HasAvailableLocalFlags}}
+
+Flags:
+{{.LocalFlags.FlagUsages | trimTrailingWhitespaces}}{{end}}{{if .HasAvailableInheritedFlags}}
+
+Global Flags:
+{{.InheritedFlags.FlagUsages | trimTrailingWhitespaces}}{{end}}{{if .HasHelpSubCommands}}
+
+Additional help topics:{{range .Commands}}{{if .IsAdditionalHelpTopicCommand}}
+  {{rpad .CommandPath .CommandPathPadding}} {{.Short}}{{end}}{{end}}{{end}}{{if .HasAvailableSubCommands}}
+
+Use "{{.CommandPath}} [command] --help" for more information about a command.{{end}}
+`)
+
+	// Add examples
+	rootCmd.Example = `  Regex mode (default):
+    modifier "<value>(\\d+)</value>" "*1.5" data.xml
+
+  JSON mode:
+    modifier -json data.json
+
+  YAML to TOML conversion:
+    modifier -conv *.yml
+    modifier -conv **/*.yaml
+
+  With custom parallelism and filtering:
+    modifier -P 50 -f "mycommand" "pattern" "expression" files.txt
+
+Note: v1, v2, etc. are used to refer to capture groups as numbers.
+      s1, s2, etc. are used to refer to capture groups as strings.
+      Helper functions: num(str) converts string to number, str(num) converts number to string
+      is_number(str) checks if a string is numeric
+      If expression starts with an operator like *, /, +, -, =, etc., v1 is automatically prepended
+      You can use any valid Lua code, including if statements, loops, etc.
+      Glob patterns are supported for file selection (*.xml, data/**.xml, etc.)
+
+` + processor.GetLuaFunctionsHelp()
+}
+
+func main() {
+	if err := rootCmd.Execute(); err != nil {
+		mainLogger.Error("Command execution failed: %v", err)
+		os.Exit(1)
+	}
+}
+
+func runModifier(args []string, cmd *cobra.Command) {
+	// Get flag values from Cobra
+	convertFlag, _ := cmd.Flags().GetBool("conv")
+	parallelFlag, _ := cmd.Flags().GetInt("parallel")
+	filterFlag, _ := cmd.Flags().GetString("filter")
+	jsonFlag, _ := cmd.Flags().GetBool("json")
 
 	// Handle YAML to TOML conversion if -conv flag is set
-	if *utils.Convert {
+	if convertFlag {
 		mainLogger.Info("YAML to TOML conversion mode enabled")
 		conversionCount := 0
 		for _, arg := range args {
@@ -127,7 +188,7 @@ func main() {
 	commands, err := utils.LoadCommands(args)
 	if err != nil || len(commands) == 0 {
 		mainLogger.Error("Failed to load commands: %v", err)
-		flag.Usage()
+		cmd.Usage()
 		return
 	}
 	// Collect global modifiers from special entries and filter them out
@@ -149,9 +210,9 @@ func main() {
 	commands = filtered
 	mainLogger.Info("Loaded %d commands", len(commands))
 
-	if *utils.Filter != "" {
+	if filterFlag != "" {
-		mainLogger.Info("Filtering commands by name: %s", *utils.Filter)
+		mainLogger.Info("Filtering commands by name: %s", filterFlag)
-		commands = utils.FilterCommands(commands, *utils.Filter)
+		commands = utils.FilterCommands(commands, filterFlag)
 		mainLogger.Info("Filtered %d commands", len(commands))
 	}
 
@@ -221,9 +282,9 @@ func main() {
 	mainLogger.Debug("Files reset where necessary")
 
 	// Then for each file run all commands associated with the file
-	workers := make(chan struct{}, *utils.ParallelFiles)
+	workers := make(chan struct{}, parallelFlag)
 	wg := sync.WaitGroup{}
-	mainLogger.Debug("Starting file processing with %d parallel workers", *utils.ParallelFiles)
+	mainLogger.Debug("Starting file processing with %d parallel workers", parallelFlag)
 
 	// Add performance tracking
 	startTime := time.Now()
@@ -273,7 +334,7 @@ func main() {
 
 			isChanged := false
 			mainLogger.Debug("Running isolate commands for file %q", file)
-			fileDataStr, err = RunIsolateCommands(association, file, fileDataStr)
+			fileDataStr, err = RunIsolateCommands(association, file, fileDataStr, jsonFlag)
 			if err != nil && err != NothingToDo {
 				mainLogger.Error("Failed to run isolate commands for file %q: %v", file, err)
 				atomic.AddInt64(&stats.FailedFiles, 1)
@@ -284,7 +345,7 @@ func main() {
 			}
 
 			mainLogger.Debug("Running other commands for file %q", file)
-			fileDataStr, err = RunOtherCommands(file, fileDataStr, association, commandLoggers)
+			fileDataStr, err = RunOtherCommands(file, fileDataStr, association, commandLoggers, jsonFlag)
 			if err != nil && err != NothingToDo {
 				mainLogger.Error("Failed to run other commands for file %q: %v", file, err)
 				atomic.AddInt64(&stats.FailedFiles, 1)
@@ -333,40 +394,6 @@ func main() {
 	// Do that with logger.WithField("loglevel", level.String())
 	// Since each command also has its own log level
 	// TODO: Maybe even figure out how to run individual commands...?
-	// TODO: What to do with git? Figure it out ....
-
-	// if *gitFlag {
-	// 	mainLogger.Info("Git integration enabled, setting up git repository")
-	// 	err := setupGit()
-	// 	if err != nil {
-	// 		mainLogger.Error("Failed to setup git: %v", err)
-	// 		fmt.Fprintf(os.Stderr, "Error setting up git: %v\n", err)
-	// 		return
-	// 	}
-	// }
-
-	// mainLogger.Debug("Expanding file patterns")
-	// files, err := expandFilePatterns(filePatterns)
-	// if err != nil {
-	// 	mainLogger.Error("Failed to expand file patterns: %v", err)
-	// 	fmt.Fprintf(os.Stderr, "Error expanding file patterns: %v\n", err)
-	// 	return
-	// }
-
-	// if *gitFlag {
-	// 	mainLogger.Info("Cleaning up git files before processing")
-	// 	err := cleanupGitFiles(files)
-	// 	if err != nil {
-	// 		mainLogger.Error("Failed to cleanup git files: %v", err)
-	// 		fmt.Fprintf(os.Stderr, "Error cleaning up git files: %v\n", err)
-	// 		return
-	// 	}
-	// }
-	// if *resetFlag {
-	// 	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
 	totalModifications := atomic.LoadInt64(&stats.TotalModifications)
@@ -444,7 +471,7 @@ func CreateExampleConfig() {
 
 var NothingToDo = errors.New("nothing to do")
 
-func RunOtherCommands(file string, fileDataStr string, association utils.FileCommandAssociation, commandLoggers map[string]*logger.Logger) (string, error) {
+func RunOtherCommands(file string, fileDataStr string, association utils.FileCommandAssociation, commandLoggers map[string]*logger.Logger, jsonFlag bool) (string, error) {
 	runOtherCommandsLogger := mainLogger.WithPrefix("RunOtherCommands").WithField("file", file)
 	runOtherCommandsLogger.Debug("Running other commands for file")
 	runOtherCommandsLogger.Trace("File data before modifications: %s", utils.LimitString(fileDataStr, 200))
@@ -454,7 +481,7 @@ func RunOtherCommands(file string, fileDataStr string, association utils.FileCom
 	regexCommands := []utils.ModifyCommand{}
 
 	for _, command := range association.Commands {
-		if command.JSON || *utils.JSON {
+		if command.JSON || jsonFlag {
 			jsonCommands = append(jsonCommands, command)
 		} else {
 			regexCommands = append(regexCommands, command)
@@ -548,7 +575,7 @@ func RunOtherCommands(file string, fileDataStr string, association utils.FileCom
 	return fileDataStr, nil
 }
 
-func RunIsolateCommands(association utils.FileCommandAssociation, file string, fileDataStr string) (string, error) {
+func RunIsolateCommands(association utils.FileCommandAssociation, file string, fileDataStr string, jsonFlag bool) (string, error) {
 	runIsolateCommandsLogger := mainLogger.WithPrefix("RunIsolateCommands").WithField("file", file)
 	runIsolateCommandsLogger.Debug("Running isolate commands for file")
 	runIsolateCommandsLogger.Trace("File data before isolate modifications: %s", utils.LimitString(fileDataStr, 200))
@@ -558,7 +585,7 @@ func RunIsolateCommands(association utils.FileCommandAssociation, file string, f
 
 	for _, isolateCommand := range association.IsolateCommands {
 		// Check if this isolate command should use JSON mode
-		if isolateCommand.JSON || *utils.JSON {
+		if isolateCommand.JSON || jsonFlag {
 			runIsolateCommandsLogger.Debug("Begin processing file with JSON isolate command %q", isolateCommand.Name)
 			modifications, err := processor.ProcessJSON(currentFileData, isolateCommand, file)
 			if err != nil {

processor/regex.go

@@ -53,7 +53,7 @@ func ProcessRegex(content string, command utils.ModifyCommand, filename string)
 		processRegexLogger.Error("Error compiling pattern %q: %v", pattern, err)
 		return commands, fmt.Errorf("error compiling pattern: %v", err)
 	}
-	processRegexLogger.Debug("Compiled pattern successfully in %v", time.Since(patternCompileStart))
+	processRegexLogger.Debug("Compiled pattern successfully in %v. Pattern: %s", time.Since(patternCompileStart), pattern)
 
 	// Same here, it's just string concatenation, it won't kill us
 	// More important is that we don't fuck up the command
@@ -77,7 +77,7 @@ func ProcessRegex(content string, command utils.ModifyCommand, filename string)
 	processRegexLogger.Debug("Pattern complexity estimate: %d", patternComplexity)
 
 	if len(indices) == 0 {
-		processRegexLogger.Warning("No matches found for regex: %q", pattern)
+		processRegexLogger.Warning("No matches found for regex: %s", pattern)
 		processRegexLogger.Debug("Total regex processing time: %v", time.Since(startTime))
 		return commands, nil
 	}
@@ -335,6 +335,9 @@ func resolveRegexPlaceholders(pattern string) string {
 	pattern = strings.ReplaceAll(pattern, "!any", `.*?`)
 	resolveLogger.Debug("Replaced !any with non-greedy wildcard")
 
+	pattern = strings.ReplaceAll(pattern, "\n", "\r?\n")
+	resolveLogger.Debug("Added optional carriage return support for Windows line endings")
+
 	repPattern := regexp.MustCompile(`!rep\(([^,]+),\s*(\d+)\)`)
 	// !rep(pattern, count) repeats the pattern n times
 	// Inserting !any between each repetition

utils/flags.go

@@ -1,23 +0,0 @@
-package utils
-
-import (
-	"flag"
-
-	logger "git.site.quack-lab.dev/dave/cylogger"
-)
-
-// flagsLogger is a scoped logger for the utils/flags package.
-var flagsLogger = logger.Default.WithPrefix("utils/flags")
-
-var (
-	ParallelFiles = flag.Int("P", 100, "Number of files to process in parallel")
-	Filter        = flag.String("f", "", "Filter commands before running them")
-	JSON          = flag.Bool("json", false, "Enable JSON mode for processing JSON files")
-	Convert       = flag.Bool("conv", false, "Convert YAML files to TOML format")
-)
-
-func init() {
-	flagsLogger.Debug("Initializing command-line flags")
-	flagsLogger.Trace("Initial flag values - ParallelFiles: %d, Filter: %q, JSON: %t, Convert: %t", *ParallelFiles, *Filter, *JSON, *Convert)
-	flagsLogger.Debug("Flag definitions: -P (parallel files), -f (filter), -json (JSON mode), -conv (YAML to TOML conversion)")
-}