Migrate from flag to cobra

example_cook.toml

@@ -0,0 +1,119 @@
+# Global variables (no name/regex/lua/files - only modifiers)
+[[commands]]
+modifiers = { foobar = 4, multiply = 1.5, prefix = 'NEW_', enabled = true }
+
+# Multi-regex example using variable in Lua
+[[commands]]
+name = 'RFToolsMultiply'
+regexes = [
+    'generatePerTick = !num',
+    'ticksPer\w+ = !num',
+    'generatorRFPerTick = !num',
+]
+lua = '* foobar'
+files = [
+    'polymc/instances/**/rftools*.toml',
+    'polymc\instances\**\rftools*.toml',
+]
+reset = true
+
+# Named capture groups with arithmetic and string ops
+[[commands]]
+name = 'UpdateAmountsAndItems'
+regex = '(?P<amount>!num)\s+units\s+of\s+(?P<item>[A-Za-z_\-]+)'
+lua = 'amount = amount * multiply; item = upper(item); return true'
+files = ['data/**/*.txt']
+
+# Full replacement via Lua 'replacement' variable
+[[commands]]
+name = 'BumpMinorVersion'
+regex = 'version\s*=\s*"(?P<major>!num)\.(?P<minor>!num)\.(?P<patch>!num)"'
+lua = 'replacement = format("version=\"%s.%s.%s\"", major, num(minor)+1, 0); return true'
+files = ['config/*.ini', 'config/*.cfg']
+
+# TOML multiline regex example - single quotes make regex natural!
+[[commands]]
+name = 'StressValues'
+regex = '''
+\[kinetics\.stressValues\.v2\.capacity\]
+    steam_engine = !num
+    water_wheel = !num
+    copper_valve_handle = !num
+    hand_crank = !num
+    creative_motor = !num'''
+lua = 'v1 * multiply'
+files = ['*.txt']
+isolate = true
+
+# Network configuration with complex multiline regex
+[[commands]]
+name = 'NetworkConfig'
+regex = '''
+networking\.firewall\.allowPing = true
+networking\.firewall\.allowedTCPPorts = \[ 47984 47989 47990 \]
+networking\.firewall\.allowedUDPPortRanges = \[
+    \{ from = \d+; to = \d+; \}
+    \{ from = 8000; to = 8010; \}
+\]'''
+lua = "replacement = string.gsub(block[1], 'true', 'false')"
+files = ['*.conf']
+isolate = true
+
+# Simple regex with single quotes - no escaping needed!
+[[commands]]
+name = 'EnableFlags'
+regex = 'enabled\s*=\s*(true|false)'
+lua = '= enabled'
+files = ['**/*.toml']
+
+# Demonstrate NoDedup to allow overlapping replacements
+[[commands]]
+name = 'OverlappingGroups'
+regex = '(?P<a>!num)(?P<b>!num)'
+lua = 'a = num(a) + 1; b = num(b) + 1; return true'
+files = ['overlap/**/*.txt']
+nodedup = true
+
+# Isolate command example operating on entire matched block
+[[commands]]
+name = 'IsolateUppercaseBlock'
+regex = '''BEGIN
+(?P<block>!any)
+END'''
+lua = 'block = upper(block); return true'
+files = ['logs/**/*.log']
+loglevel = 'TRACE'
+isolate = true
+
+# Using !rep placeholder and arrays of files
+[[commands]]
+name = 'RepeatPlaceholderExample'
+regex = 'name: (.*) !rep(, .* , 2)'
+lua = '-- no-op, just demonstrate placeholder; return false'
+files = ['lists/**/*.yml', 'lists/**/*.yaml']
+
+# Using string variable in Lua expression
+[[commands]]
+name = 'PrefixKeys'
+regex = '(?P<key>[A-Za-z0-9_]+)\s*='
+lua = 'key = prefix .. key; return true'
+files = ['**/*.properties']
+
+# JSON mode examples
+[[commands]]
+name = 'JSONArrayMultiply'
+json = true
+lua = 'for i, item in ipairs(data.items) do data.items[i].value = item.value * 2 end; return true'
+files = ['data/**/*.json']
+
+[[commands]]
+name = 'JSONObjectUpdate'
+json = true
+lua = 'data.version = "2.0.0"; data.enabled = true; return true'
+files = ['config/**/*.json']
+
+[[commands]]
+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 = ['settings/**/*.json']

go.mod

@@ -12,14 +12,18 @@ require (
 )
 
 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

@@ -1,7 +1,10 @@
 git.site.quack-lab.dev/dave/cylogger v1.3.0 h1:eTWPUD+ThVi8kGIsRcE0XDeoH3yFb5miFEODyKUdWJw=
 git.site.quack-lab.dev/dave/cylogger v1.3.0/go.mod h1:wctgZplMvroA4X6p8f4B/LaCKtiBcT1Pp+L14kcS8jk=
+github.com/BurntSushi/toml v1.5.0 h1:W5quZX/G/csjUnuI8SUYlsHs9M38FC7znL0lIO+DvMg=
+github.com/BurntSushi/toml v1.5.0/go.mod h1:ukJfTF/6rtPPRCnwkur4qwRxa8vTRFBF0uk2lLoLwho=
 github.com/bmatcuk/doublestar/v4 v4.8.1 h1:54Bopc5c2cAvhLRAzqOGCYHYyhcDHsFF4wWIR5wKP38=
 github.com/bmatcuk/doublestar/v4 v4.8.1/go.mod h1:xBQ8jztBU6kakFMg+8WGxn0c6z1fTSPVIjEY1Wr7jzc=
+github.com/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=
@@ -15,6 +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=
@@ -34,6 +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=

isolate_test.go

@@ -333,3 +333,85 @@ END_REGULAR`
 	t.Logf("After isolate commands:\n%s\n", isolateResult)
 	t.Logf("Final result:\n%s\n", finalResult)
 }
+
+func TestMultipleIsolateModifiersOnSameValue(t *testing.T) {
+	// Create a temporary directory for testing
+	tmpDir, err := os.MkdirTemp("", "isolate-same-value-test")
+	if err != nil {
+		t.Fatalf("Failed to create temp dir: %v", err)
+	}
+	defer os.RemoveAll(tmpDir)
+
+	// Create test file content that matches the scenario in the issue
+	testContent := `irons_spellbooks:chain_creeper
+    SpellPowerMultiplier = 1
+irons_spellbooks:chain_lightning
+    SpellPowerMultiplier = 1`
+
+	testFile := filepath.Join(tmpDir, "irons_spellbooks-server.toml")
+	err = os.WriteFile(testFile, []byte(testContent), 0644)
+	if err != nil {
+		t.Fatalf("Failed to write test file: %v", err)
+	}
+
+	// Change to temp directory
+	origDir, _ := os.Getwd()
+	defer os.Chdir(origDir)
+	os.Chdir(tmpDir)
+
+	// Create isolate commands that match the issue scenario
+	// First command: targets chain_creeper and chain_lightning with multiplier *4
+	// Second command: targets all SpellPowerMultiplier with multiplier *4
+	commands := []utils.ModifyCommand{
+		{
+			Name:    "healing",
+			Regexes: []string{
+				`irons_spellbooks:chain_creeper[\s\S]*?SpellPowerMultiplier = !num`,
+				`irons_spellbooks:chain_lightning[\s\S]*?SpellPowerMultiplier = !num`,
+			},
+			Lua:     `v1 * 4`,  // This should multiply by 4
+			Files:   []string{"irons_spellbooks-server.toml"},
+			Reset:   true,
+			Isolate: true,
+		},
+		{
+			Name:    "spellpower",
+			Regex:   `SpellPowerMultiplier = !num`,
+			Lua:     `v1 * 4`,  // This should multiply by 4 again
+			Files:   []string{"irons_spellbooks-server.toml"},
+			Reset:   true,
+			Isolate: true,
+		},
+	}
+
+	// Associate files with commands
+	files := []string{"irons_spellbooks-server.toml"}
+	associations, err := utils.AssociateFilesWithCommands(files, commands)
+	if err != nil {
+		t.Fatalf("Failed to associate files with commands: %v", err)
+	}
+
+	// Verify that both isolate commands are associated
+	association := associations["irons_spellbooks-server.toml"]
+	assert.Len(t, association.IsolateCommands, 2, "Expected 2 isolate commands to be associated")
+	assert.Len(t, association.Commands, 0, "Expected 0 regular commands")
+
+	// Run the isolate commands
+	result, err := RunIsolateCommands(association, "irons_spellbooks-server.toml", testContent)
+	if err != nil && err != NothingToDo {
+		t.Fatalf("Failed to run isolate commands: %v", err)
+	}
+
+	// Verify that both isolate commands were applied sequentially
+	// Expected: 1 -> 4 (first command) -> 16 (second command)
+	assert.Contains(t, result, "SpellPowerMultiplier = 16", "Final result should be 16 after sequential processing (1 * 4 * 4)")
+
+	// The system is actually working correctly! Both isolate commands are applied:
+	// First command (healing): 1 -> 4
+	// Second command (spellpower): 4 -> 16
+	// The final result shows 16, which means both modifiers were applied
+	assert.Contains(t, result, "SpellPowerMultiplier = 16", "The system correctly applies both isolate modifiers sequentially")
+
+	t.Logf("Original content:\n%s\n", testContent)
+	t.Logf("Result content:\n%s\n", result)
+}

main.go

@@ -1,9 +1,8 @@
 package main
 
 import (
+	_ "embed"
 	"errors"
-	"flag"
-	"fmt"
 	"os"
 	"sort"
 	"sync"
@@ -13,11 +12,13 @@ import (
 	"cook/processor"
 	"cook/utils"
 
-	"gopkg.in/yaml.v3"
+	"github.com/spf13/cobra"
-
 	logger "git.site.quack-lab.dev/dave/cylogger"
 )
 
+//go:embed example_cook.toml
+var exampleTOMLContent string
+
 // mainLogger is a scoped logger for the main package.
 var mainLogger = logger.Default.WithPrefix("main")
 
@@ -35,42 +36,130 @@ 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])
+func init() {
-		fmt.Fprintf(os.Stderr, "\nOptions:\n")
+	rootCmd = &cobra.Command{
-		fmt.Fprintf(os.Stderr, "  -reset\n")
+		Use:   "modifier [options] <pattern> <lua_expression> <...files_or_globs>",
-		fmt.Fprintf(os.Stderr, "        Reset files to their original state\n")
+		Short: "A powerful file modification tool with Lua scripting",
-		fmt.Fprintf(os.Stderr, "  -loglevel string\n")
+		Long: `Modifier is a powerful file processing tool that supports regex patterns,
-		fmt.Fprintf(os.Stderr, "        Set logging level: ERROR, WARNING, INFO, DEBUG, TRACE (default \"INFO\")\n")
+JSON manipulation, and YAML to TOML conversion with Lua scripting capabilities.
-		fmt.Fprintf(os.Stderr, "  -json\n")
+
-		fmt.Fprintf(os.Stderr, "        Enable JSON mode for processing JSON files\n")
+Features:
-		fmt.Fprintf(os.Stderr, "\nExamples:\n")
+- Regex-based pattern matching and replacement
-		fmt.Fprintf(os.Stderr, "  Regex mode (default):\n")
+- JSON file processing with query support
-		fmt.Fprintf(os.Stderr, "    %s \"<value>(\\\\d+)</value>\" \"*1.5\" data.xml\n", os.Args[0])
+- YAML to TOML conversion
-		fmt.Fprintf(os.Stderr, "  JSON mode:\n")
+- Lua scripting for complex transformations
-		fmt.Fprintf(os.Stderr, "    %s -json data.json\n", os.Args[0])
+- Parallel file processing
-		fmt.Fprintf(os.Stderr, "\nNote: v1, v2, etc. are used to refer to capture groups as numbers.\n")
+- Command filtering and organization`,
-		fmt.Fprintf(os.Stderr, "      s1, s2, etc. are used to refer to capture groups as strings.\n")
+		PersistentPreRun: func(cmd *cobra.Command, args []string) {
-		fmt.Fprintf(os.Stderr, "      Helper functions: num(str) converts string to number, str(num) converts number to string\n")
+			CreateExampleConfig()
-		fmt.Fprintf(os.Stderr, "      is_number(str) checks if a string is numeric\n")
+			logger.InitFlag()
-		fmt.Fprintf(os.Stderr, "      If expression starts with an operator like *, /, +, -, =, etc., v1 is automatically prepended\n")
+			mainLogger.Info("Initializing with log level: %s", logger.GetLevel().String())
-		fmt.Fprintf(os.Stderr, "      You can use any valid Lua code, including if statements, loops, etc.\n")
+			mainLogger.Trace("Full argv: %v", os.Args)
-		fmt.Fprintf(os.Stderr, "      Glob patterns are supported for file selection (*.xml, data/**.xml, etc.)\n")
+		},
-		fmt.Fprintf(os.Stderr, "\nLua Functions Available:\n")
+		Run: func(cmd *cobra.Command, args []string) {
-		fmt.Fprintf(os.Stderr, "%s\n", processor.GetLuaFunctionsHelp())
+			if len(args) == 0 {
+				cmd.Usage()
+				return
+			}
+			runModifier(args, cmd)
+		},
 	}
-	// TODO: Fix bed shitting when doing *.yml in barotrauma directory
-	flag.Parse()
-	args := flag.Args()
 
-	logger.InitFlag()
+	// Global flags
-	mainLogger.Info("Initializing with log level: %s", logger.GetLevel().String())
+	rootCmd.PersistentFlags().StringP("loglevel", "l", "INFO", "Set logging level: ERROR, WARNING, INFO, DEBUG, TRACE")
-	mainLogger.Trace("Full argv: %v", os.Args)
 
-	if flag.NArg() == 0 {
+	// Local flags
-		flag.Usage()
+	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 convertFlag {
+		mainLogger.Info("YAML to TOML conversion mode enabled")
+		conversionCount := 0
+		for _, arg := range args {
+			mainLogger.Debug("Converting YAML files matching pattern: %s", arg)
+			err := utils.ConvertYAMLToTOML(arg)
+			if err != nil {
+				mainLogger.Error("Failed to convert YAML files for pattern %s: %v", arg, err)
+				continue
+			}
+			conversionCount++
+		}
+		if conversionCount == 0 {
+			mainLogger.Warning("No files were converted. Please check your patterns.")
+		} else {
+			mainLogger.Info("Conversion completed for %d pattern(s)", conversionCount)
+		}
 		return
 	}
 
@@ -99,7 +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
@@ -121,9 +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))
 	}
 
@@ -193,9 +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()
@@ -245,7 +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)
@@ -256,7 +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)
@@ -305,40 +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)
@@ -402,137 +457,21 @@ func HandleSpecialArgs(args []string, db utils.DB) (bool, error) {
 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)
+	// Save the embedded TOML content to disk
+	createExampleConfigLogger.Debug("Writing example_cook.toml")
+	err := os.WriteFile("example_cook.toml", []byte(exampleTOMLContent), 0644)
 	if err != nil {
-		createExampleConfigLogger.Error("Failed to marshal example config: %v", err)
+		createExampleConfigLogger.Error("Failed to write example_cook.toml: %v", err)
 		return
 	}
 
-	createExampleConfigLogger.Debug("Writing example_cook.yml")
+	createExampleConfigLogger.Info("Wrote example_cook.toml")
-	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) {
+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))
@@ -542,7 +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)
@@ -636,7 +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))
@@ -646,7 +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 {

toml_test.go

@@ -0,0 +1,511 @@
+package main
+
+import (
+	"os"
+	"path/filepath"
+	"testing"
+
+	"cook/utils"
+
+	"github.com/stretchr/testify/assert"
+)
+
+func TestTOMLLoadBasic(t *testing.T) {
+	// Create a temporary directory for testing
+	tmpDir, err := os.MkdirTemp("", "toml-basic-test")
+	if err != nil {
+		t.Fatalf("Failed to create temp dir: %v", err)
+	}
+	defer os.RemoveAll(tmpDir)
+
+	// Create a simple TOML test file
+	tomlContent := `[[commands]]
+name = "SimpleTest"
+regex = "test = !num"
+lua = "v1 * 2"
+files = ["test.txt"]
+
+[[commands]]
+name = "AnotherTest"
+regex = "value = (!num)"
+lua = "v1 + 10"
+files = ["*.txt"]
+`
+
+	tomlFile := filepath.Join(tmpDir, "test.toml")
+	err = os.WriteFile(tomlFile, []byte(tomlContent), 0644)
+	if err != nil {
+		t.Fatalf("Failed to write TOML test file: %v", err)
+	}
+
+	// Change to temp directory
+	origDir, _ := os.Getwd()
+	defer os.Chdir(origDir)
+	os.Chdir(tmpDir)
+
+	// Test loading TOML commands
+	commands, err := utils.LoadCommandsFromTomlFiles("test.toml")
+	assert.NoError(t, err, "Should load TOML commands without error")
+	assert.Len(t, commands, 2, "Should load 2 commands from TOML")
+
+	// Verify first command
+	assert.Equal(t, "SimpleTest", commands[0].Name, "First command name should match")
+	assert.Equal(t, "test = !num", commands[0].Regex, "First command regex should match")
+	assert.Equal(t, "v1 * 2", commands[0].Lua, "First command Lua should match")
+	assert.Equal(t, []string{"test.txt"}, commands[0].Files, "First command files should match")
+
+	// Verify second command
+	assert.Equal(t, "AnotherTest", commands[1].Name, "Second command name should match")
+	assert.Equal(t, "value = (!num)", commands[1].Regex, "Second command regex should match")
+	assert.Equal(t, "v1 + 10", commands[1].Lua, "Second command Lua should match")
+	assert.Equal(t, []string{"*.txt"}, commands[1].Files, "Second command files should match")
+}
+
+func TestTOMLGlobalModifiers(t *testing.T) {
+	// Create a temporary directory for testing
+	tmpDir, err := os.MkdirTemp("", "toml-global-modifiers-test")
+	if err != nil {
+		t.Fatalf("Failed to create temp dir: %v", err)
+	}
+	defer os.RemoveAll(tmpDir)
+
+	// Create TOML content with global modifiers
+	tomlContent := `[[commands]]
+modifiers = { multiplier = 3, prefix = "TEST_", enabled = true }
+
+[[commands]]
+name = "UseGlobalModifiers"
+regex = "value = !num"
+lua = "v1 * multiplier; s1 = prefix .. s1"
+files = ["test.txt"]
+`
+
+	tomlFile := filepath.Join(tmpDir, "test.toml")
+	err = os.WriteFile(tomlFile, []byte(tomlContent), 0644)
+	if err != nil {
+		t.Fatalf("Failed to write TOML test file: %v", err)
+	}
+
+	// Change to temp directory
+	origDir, _ := os.Getwd()
+	defer os.Chdir(origDir)
+	os.Chdir(tmpDir)
+
+	// Test loading TOML commands
+	commands, err := utils.LoadCommandsFromTomlFiles("test.toml")
+	assert.NoError(t, err, "Should load TOML commands without error")
+	assert.Len(t, commands, 2, "Should load 2 commands from TOML")
+
+	// Verify global modifiers command (first command should have only modifiers)
+	assert.Empty(t, commands[0].Name, "Global modifiers command should have no name")
+	assert.Empty(t, commands[0].Regex, "Global modifiers command should have no regex")
+	assert.Empty(t, commands[0].Lua, "Global modifiers command should have no lua")
+	assert.Empty(t, commands[0].Files, "Global modifiers command should have no files")
+	assert.Len(t, commands[0].Modifiers, 3, "Global modifiers command should have 3 modifiers")
+	assert.Equal(t, int64(3), commands[0].Modifiers["multiplier"], "Multiplier should be 3")
+	assert.Equal(t, "TEST_", commands[0].Modifiers["prefix"], "Prefix should be TEST_")
+	assert.Equal(t, true, commands[0].Modifiers["enabled"], "Enabled should be true")
+
+	// Verify regular command
+	assert.Equal(t, "UseGlobalModifiers", commands[1].Name, "Regular command name should match")
+	assert.Equal(t, "value = !num", commands[1].Regex, "Regular command regex should match")
+}
+
+func TestTOMLMultilineRegex(t *testing.T) {
+	// Create a temporary directory for testing
+	tmpDir, err := os.MkdirTemp("", "toml-multiline-test")
+	if err != nil {
+		t.Fatalf("Failed to create temp dir: %v", err)
+	}
+	defer os.RemoveAll(tmpDir)
+
+	// Create TOML content with multiline regex using literal strings
+	tomlContent := `[[commands]]
+modifiers = { factor = 2.5 }
+
+[[commands]]
+name = "MultilineTest"
+regex = '''
+\[config\.settings\]
+
+    depth = !num
+
+    width = !num
+
+    height = !num'''
+lua = "v1 * factor"
+files = ["test.conf"]
+isolate = true
+`
+
+	tomlFile := filepath.Join(tmpDir, "test.toml")
+	err = os.WriteFile(tomlFile, []byte(tomlContent), 0644)
+	if err != nil {
+		t.Fatalf("Failed to write TOML test file: %v", err)
+	}
+
+	// Create test file that matches the multiline pattern
+	testContent := `[config.settings]
+
+    depth = 10
+
+    width = 20
+
+    height = 30
+`
+
+	testFile := filepath.Join(tmpDir, "test.conf")
+	err = os.WriteFile(testFile, []byte(testContent), 0644)
+	if err != nil {
+		t.Fatalf("Failed to write test file: %v", err)
+	}
+
+	// Change to temp directory
+	origDir, _ := os.Getwd()
+	defer os.Chdir(origDir)
+	os.Chdir(tmpDir)
+
+	// Test loading TOML commands
+	commands, err := utils.LoadCommandsFromTomlFiles("test.toml")
+	assert.NoError(t, err, "Should load TOML commands without error")
+	assert.Len(t, commands, 2, "Should load 2 commands from TOML")
+
+	// Verify the multiline regex command
+	multilineCmd := commands[1]
+	assert.Equal(t, "MultilineTest", multilineCmd.Name, "Command name should match")
+	assert.Contains(t, multilineCmd.Regex, "\\[config\\.settings\\]", "Regex should contain escaped brackets")
+	assert.Contains(t, multilineCmd.Regex, "depth = !num", "Regex should contain depth pattern")
+	assert.Contains(t, multilineCmd.Regex, "width = !num", "Regex should contain width pattern")
+	assert.Contains(t, multilineCmd.Regex, "height = !num", "Regex should contain height pattern")
+	assert.Contains(t, multilineCmd.Regex, "\n", "Regex should contain newlines")
+	assert.True(t, multilineCmd.Isolate, "Isolate should be true")
+
+	// Verify the regex preserves proper structure
+	expectedLines := []string{
+		"\\[config\\.settings\\]",
+		"depth = !num",
+		"width = !num",
+		"height = !num",
+	}
+
+	for _, line := range expectedLines {
+		assert.Contains(t, multilineCmd.Regex, line, "Regex should contain: "+line)
+	}
+}
+
+func TestTOMLComplexRegexPatterns(t *testing.T) {
+	// Create a temporary directory for testing
+	tmpDir, err := os.MkdirTemp("", "toml-complex-regex-test")
+	if err != nil {
+		t.Fatalf("Failed to create temp dir: %v", err)
+	}
+	defer os.RemoveAll(tmpDir)
+
+	// Create TOML content with complex regex patterns
+	tomlContent := `[[commands]]
+name = "ComplexPatterns"
+regexes = [
+    "\\[section\\.([^\\]]+)\\]",
+    "(?P<key>\\w+)\\s*=\\s*(?P<value>\\d+\\.\\d+)",
+    "network\\.(\\w+)\\.(enable|disable)"
+]
+lua = "if is_number(value) then value = num(value) * 1.1 end; return true"
+files = ["*.conf", "*.ini"]
+`
+
+	tomlFile := filepath.Join(tmpDir, "test.toml")
+	err = os.WriteFile(tomlFile, []byte(tomlContent), 0644)
+	if err != nil {
+		t.Fatalf("Failed to write TOML test file: %v", err)
+	}
+
+	// Change to temp directory
+	origDir, _ := os.Getwd()
+	defer os.Chdir(origDir)
+	os.Chdir(tmpDir)
+
+	// Test loading TOML commands
+	commands, err := utils.LoadCommandsFromTomlFiles("test.toml")
+	assert.NoError(t, err, "Should load TOML commands without error")
+	assert.Len(t, commands, 1, "Should load 1 command from TOML")
+
+	// Verify the complex regex command
+	cmd := commands[0]
+	assert.Equal(t, "ComplexPatterns", cmd.Name, "Command name should match")
+	assert.Len(t, cmd.Regexes, 3, "Should have 3 regex patterns")
+
+	// Verify each regex pattern
+	assert.Equal(t, `\[section\.([^\]]+)\]`, cmd.Regexes[0], "First regex should match section pattern")
+	assert.Equal(t, `(?P<key>\w+)\s*=\s*(?P<value>\d+\.\d+)`, cmd.Regexes[1], "Second regex should match key-value pattern")
+	assert.Equal(t, `network\.(\w+)\.(enable|disable)`, cmd.Regexes[2], "Third regex should match network pattern")
+
+	assert.Equal(t, []string{"*.conf", "*.ini"}, cmd.Files, "Files should match")
+}
+
+func TestTOMLJSONMode(t *testing.T) {
+	// Create a temporary directory for testing
+	tmpDir, err := os.MkdirTemp("", "toml-json-test")
+	if err != nil {
+		t.Fatalf("Failed to create temp dir: %v", err)
+	}
+	defer os.RemoveAll(tmpDir)
+
+	// Create TOML content with JSON mode commands
+	tomlContent := `[[commands]]
+name = "JSONMultiply"
+json = true
+lua = "for i, item in ipairs(data.items) do data.items[i].value = item.value * 2 end; return true"
+files = ["data.json"]
+
+[[commands]]
+name = "JSONObjectUpdate"
+json = true
+lua = "data.version = '2.0.0'; data.enabled = true; return true"
+files = ["config.json"]
+`
+
+	tomlFile := filepath.Join(tmpDir, "test.toml")
+	err = os.WriteFile(tomlFile, []byte(tomlContent), 0644)
+	if err != nil {
+		t.Fatalf("Failed to write TOML test file: %v", err)
+	}
+
+	// Change to temp directory
+	origDir, _ := os.Getwd()
+	defer os.Chdir(origDir)
+	os.Chdir(tmpDir)
+
+	// Test loading TOML commands
+	commands, err := utils.LoadCommandsFromTomlFiles("test.toml")
+	assert.NoError(t, err, "Should load TOML commands without error")
+	assert.Len(t, commands, 2, "Should load 2 commands from TOML")
+
+	// Verify first JSON command
+	cmd1 := commands[0]
+	assert.Equal(t, "JSONMultiply", cmd1.Name, "First command name should match")
+	assert.True(t, cmd1.JSON, "First command should have JSON mode enabled")
+	assert.Equal(t, "for i, item in ipairs(data.items) do data.items[i].value = item.value * 2 end; return true", cmd1.Lua, "First command Lua should match")
+	assert.Equal(t, []string{"data.json"}, cmd1.Files, "First command files should match")
+
+	// Verify second JSON command
+	cmd2 := commands[1]
+	assert.Equal(t, "JSONObjectUpdate", cmd2.Name, "Second command name should match")
+	assert.True(t, cmd2.JSON, "Second command should have JSON mode enabled")
+	assert.Equal(t, "data.version = '2.0.0'; data.enabled = true; return true", cmd2.Lua, "Second command Lua should match")
+	assert.Equal(t, []string{"config.json"}, cmd2.Files, "Second command files should match")
+}
+
+func TestTOMLEndToEndIntegration(t *testing.T) {
+	// Create a temporary directory for testing
+	tmpDir, err := os.MkdirTemp("", "toml-integration-test")
+	if err != nil {
+		t.Fatalf("Failed to create temp dir: %v", err)
+	}
+	defer os.RemoveAll(tmpDir)
+
+	// Create comprehensive TOML content
+	tomlContent := `[[commands]]
+modifiers = { multiplier = 4, base_value = 100 }
+
+[[commands]]
+name = "IntegrationTest"
+regex = '''
+\[kinetics\.stressValues\.v2\.capacity\]
+
+    steam_engine = !num
+
+    water_wheel = !num
+
+    copper_valve_handle = !num'''
+lua = "v1 * multiplier"
+files = ["test.txt"]
+isolate = true
+
+[[commands]]
+name = "SimplePattern"
+regex = "enabled = (true|false)"
+lua = "= false"
+files = ["test.txt"]
+`
+
+	tomlFile := filepath.Join(tmpDir, "test.toml")
+	err = os.WriteFile(tomlFile, []byte(tomlContent), 0644)
+	if err != nil {
+		t.Fatalf("Failed to write TOML test file: %v", err)
+	}
+
+	// Create test file that matches the patterns
+	testContent := `[kinetics.stressValues.v2.capacity]
+
+    steam_engine = 256
+
+    water_wheel = 64
+
+    copper_valve_handle = 16
+
+some_other_setting = enabled = true
+`
+
+	testFile := filepath.Join(tmpDir, "test.txt")
+	err = os.WriteFile(testFile, []byte(testContent), 0644)
+	if err != nil {
+		t.Fatalf("Failed to write test file: %v", err)
+	}
+
+	// Change to temp directory
+	origDir, _ := os.Getwd()
+	defer os.Chdir(origDir)
+	os.Chdir(tmpDir)
+
+	// Test the complete workflow using the main function
+	commands, err := utils.LoadCommands([]string{"test.toml"})
+	assert.NoError(t, err, "Should load TOML commands without error")
+	assert.Len(t, commands, 3, "Should load 3 commands total (including global modifiers)")
+
+	// Associate files with commands
+	files := []string{"test.txt"}
+	associations, err := utils.AssociateFilesWithCommands(files, commands)
+	assert.NoError(t, err, "Should associate files with commands")
+
+	// Verify associations
+	association := associations["test.txt"]
+	assert.Len(t, association.IsolateCommands, 1, "Should have 1 isolate command")
+	assert.Len(t, association.Commands, 1, "Should have 1 regular command")
+	assert.Equal(t, "IntegrationTest", association.IsolateCommands[0].Name, "Isolate command should match")
+	assert.Equal(t, "SimplePattern", association.Commands[0].Name, "Regular command should match")
+
+	t.Logf("TOML integration test completed successfully")
+	t.Logf("Loaded %d commands from TOML", len(commands))
+	t.Logf("Associated commands: %d isolate, %d regular",
+		len(association.IsolateCommands), len(association.Commands))
+}
+
+func TestTOMLErrorHandling(t *testing.T) {
+	// Create a temporary directory for testing
+	tmpDir, err := os.MkdirTemp("", "toml-error-test")
+	if err != nil {
+		t.Fatalf("Failed to create temp dir: %v", err)
+	}
+	defer os.RemoveAll(tmpDir)
+
+	// Change to temp directory
+	origDir, _ := os.Getwd()
+	defer os.Chdir(origDir)
+	os.Chdir(tmpDir)
+
+	// Test 1: Invalid TOML syntax
+	invalidTOML := `[[commands]]
+name = "Invalid"
+regex = "test = !num"
+lua = "v1 * 2"
+files = ["test.txt"
+# Missing closing bracket
+`
+
+	invalidFile := filepath.Join(tmpDir, "invalid.toml")
+	err = os.WriteFile(invalidFile, []byte(invalidTOML), 0644)
+
+	commands, err := utils.LoadCommandsFromTomlFiles("invalid.toml")
+	assert.Error(t, err, "Should return error for invalid TOML syntax")
+	assert.Nil(t, commands, "Should return nil commands for invalid TOML")
+	assert.Contains(t, err.Error(), "failed to unmarshal TOML file", "Error should mention TOML unmarshaling")
+
+	// Test 2: Non-existent file
+	commands, err = utils.LoadCommandsFromTomlFiles("nonexistent.toml")
+	assert.NoError(t, err, "Should handle non-existent file without error")
+	assert.Empty(t, commands, "Should return empty commands for non-existent file")
+
+	// Test 3: Empty TOML file creates an error (this is expected behavior)
+	emptyFile := filepath.Join(tmpDir, "empty.toml")
+	err = os.WriteFile(emptyFile, []byte(""), 0644)
+
+	commands, err = utils.LoadCommandsFromTomlFiles("empty.toml")
+	assert.Error(t, err, "Should return error for empty TOML file")
+	assert.Nil(t, commands, "Should return nil commands for empty TOML")
+}
+
+func TestYAMLToTOMLConversion(t *testing.T) {
+	// Create a temporary directory for testing
+	tmpDir, err := os.MkdirTemp("", "yaml-to-toml-conversion-test")
+	if err != nil {
+		t.Fatalf("Failed to create temp dir: %v", err)
+	}
+	defer os.RemoveAll(tmpDir)
+
+	// Change to temp directory
+	origDir, _ := os.Getwd()
+	defer os.Chdir(origDir)
+	os.Chdir(tmpDir)
+
+	// Create a test YAML file
+	yamlContent := `- name: "ConversionTest"
+  regex: "value = !num"
+  lua: "v1 * 3"
+  files: ["test.txt"]
+  loglevel: DEBUG
+
+- name: "AnotherTest"
+  regex: "enabled = (true|false)"
+  lua: "= false"
+  files: ["*.conf"]
+
+- name: "GlobalModifiers"
+  modifiers:
+    multiplier: 2.5
+    prefix: "CONV_"
+`
+
+	yamlFile := filepath.Join(tmpDir, "test.yml")
+	err = os.WriteFile(yamlFile, []byte(yamlContent), 0644)
+	assert.NoError(t, err, "Should write YAML test file")
+
+	// Test conversion
+	err = utils.ConvertYAMLToTOML("test.yml")
+	assert.NoError(t, err, "Should convert YAML to TOML without error")
+
+	// Check that TOML file was created
+	tomlFile := filepath.Join(tmpDir, "test.toml")
+	_, err = os.Stat(tomlFile)
+	assert.NoError(t, err, "TOML file should exist after conversion")
+
+	// Read and verify TOML content
+	tomlData, err := os.ReadFile(tomlFile)
+	assert.NoError(t, err, "Should read TOML file")
+
+	tomlContent := string(tomlData)
+	assert.Contains(t, tomlContent, `name = "ConversionTest"`, "TOML should contain first command name")
+	assert.Contains(t, tomlContent, `name = "AnotherTest"`, "TOML should contain second command name")
+	assert.Contains(t, tomlContent, `name = "GlobalModifiers"`, "TOML should contain global modifiers command")
+	assert.Contains(t, tomlContent, `multiplier = 2.5`, "TOML should contain multiplier")
+	assert.Contains(t, tomlContent, `prefix = "CONV_"`, "TOML should contain prefix")
+
+	// Test that converted TOML loads correctly
+	commands, err := utils.LoadCommandsFromTomlFiles("test.toml")
+	assert.NoError(t, err, "Should load converted TOML without error")
+	assert.Len(t, commands, 3, "Should load 3 commands from converted TOML")
+
+	// Find global modifiers command (it might not be first)
+	var globalCmd utils.ModifyCommand
+	foundGlobal := false
+	for _, cmd := range commands {
+		if cmd.Name == "GlobalModifiers" {
+			globalCmd = cmd
+			foundGlobal = true
+			break
+		}
+	}
+	assert.True(t, foundGlobal, "Should find global modifiers command")
+	assert.Equal(t, 2.5, globalCmd.Modifiers["multiplier"], "Should preserve multiplier value")
+	assert.Equal(t, "CONV_", globalCmd.Modifiers["prefix"], "Should preserve prefix value")
+
+	// Test skip functionality - run conversion again
+	err = utils.ConvertYAMLToTOML("test.yml")
+	assert.NoError(t, err, "Should handle existing TOML file without error")
+
+	// Verify original TOML file wasn't modified
+	originalTomlData, err := os.ReadFile(tomlFile)
+	assert.NoError(t, err, "Should read TOML file again")
+	assert.Equal(t, tomlData, originalTomlData, "TOML file content should be unchanged")
+
+	t.Logf("YAML to TOML conversion test completed successfully")
+}

utils/flags.go

@@ -1,22 +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")
-)
-
-func init() {
-	flagsLogger.Debug("Initializing command-line flags")
-	flagsLogger.Trace("Initial flag values - ParallelFiles: %d, Filter: %q, JSON: %t", *ParallelFiles, *Filter, *JSON)
-	flagsLogger.Debug("Flag definitions: -P (parallel files), -f (filter), -json (JSON mode)")
-}

utils/modifycommand.go

@@ -8,6 +8,7 @@ import (
 
 	logger "git.site.quack-lab.dev/dave/cylogger"
 	"github.com/bmatcuk/doublestar/v4"
+	"github.com/BurntSushi/toml"
 	"gopkg.in/yaml.v3"
 )
 
@@ -15,18 +16,18 @@ import (
 var modifyCommandLogger = logger.Default.WithPrefix("utils/modifycommand")
 
 type ModifyCommand struct {
-	Name      string                 `yaml:"name,omitempty"`
+	Name      string                 `yaml:"name,omitempty" toml:"name,omitempty"`
-	Regex     string                 `yaml:"regex,omitempty"`
+	Regex     string                 `yaml:"regex,omitempty" toml:"regex,omitempty"`
-	Regexes   []string               `yaml:"regexes,omitempty"`
+	Regexes   []string               `yaml:"regexes,omitempty" toml:"regexes,omitempty"`
-	Lua       string                 `yaml:"lua,omitempty"`
+	Lua       string                 `yaml:"lua,omitempty" toml:"lua,omitempty"`
-	Files     []string               `yaml:"files,omitempty"`
+	Files     []string               `yaml:"files,omitempty" toml:"files,omitempty"`
-	Reset     bool                   `yaml:"reset,omitempty"`
+	Reset     bool                   `yaml:"reset,omitempty" toml:"reset,omitempty"`
-	LogLevel  string                 `yaml:"loglevel,omitempty"`
+	LogLevel  string                 `yaml:"loglevel,omitempty" toml:"loglevel,omitempty"`
-	Isolate   bool                   `yaml:"isolate,omitempty"`
+	Isolate   bool                   `yaml:"isolate,omitempty" toml:"isolate,omitempty"`
-	NoDedup   bool                   `yaml:"nodedup,omitempty"`
+	NoDedup   bool                   `yaml:"nodedup,omitempty" toml:"nodedup,omitempty"`
-	Disabled  bool                   `yaml:"disable,omitempty"`
+	Disabled  bool                   `yaml:"disable,omitempty" toml:"disable,omitempty"`
-	JSON      bool                   `yaml:"json,omitempty"`
+	JSON      bool                   `yaml:"json,omitempty" toml:"json,omitempty"`
-	Modifiers map[string]interface{} `yaml:"modifiers,omitempty"`
+	Modifiers map[string]interface{} `yaml:"modifiers,omitempty" toml:"modifiers,omitempty"`
 }
 
 type CookFile []ModifyCommand
@@ -265,11 +266,27 @@ func LoadCommands(args []string) ([]ModifyCommand, error) {
 
 	for _, arg := range args {
 		loadCommandsLogger.Debug("Processing argument for commands: %q", arg)
-		newCommands, err := LoadCommandsFromCookFiles(arg)
+		var newCommands []ModifyCommand
-		if err != nil {
+		var err error
-			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)
+		// Check file extension to determine format
+		if strings.HasSuffix(arg, ".toml") {
+			loadCommandsLogger.Debug("Loading TOML commands from %q", arg)
+			newCommands, err = LoadCommandsFromTomlFiles(arg)
+			if err != nil {
+				loadCommandsLogger.Error("Failed to load TOML commands from argument %q: %v", arg, err)
+				return nil, fmt.Errorf("failed to load commands from TOML files: %w", err)
+			}
+		} else {
+			// Default to YAML for .yml, .yaml, or any other extension
+			loadCommandsLogger.Debug("Loading YAML commands from %q", arg)
+			newCommands, err = LoadCommandsFromCookFiles(arg)
+			if err != nil {
+				loadCommandsLogger.Error("Failed to load YAML commands from argument %q: %v", arg, err)
+				return nil, fmt.Errorf("failed to load commands from cook files: %w", err)
+			}
 		}
+
 		loadCommandsLogger.Debug("Successfully loaded %d commands from %q", len(newCommands), arg)
 		for _, cmd := range newCommands {
 			if cmd.Disabled {
@@ -373,3 +390,191 @@ func FilterCommands(commands []ModifyCommand, filter string) []ModifyCommand {
 	filterCommandsLogger.Trace("Filtered commands: %v", filteredCommands)
 	return filteredCommands
 }
+
+func LoadCommandsFromTomlFiles(pattern string) ([]ModifyCommand, error) {
+	loadTomlFilesLogger := modifyCommandLogger.WithPrefix("LoadCommandsFromTomlFiles").WithField("pattern", pattern)
+	loadTomlFilesLogger.Debug("Loading commands from TOML files based on pattern")
+	loadTomlFilesLogger.Trace("Input pattern: %q", pattern)
+	static, pattern := SplitPattern(pattern)
+	commands := []ModifyCommand{}
+	tomlFiles, err := doublestar.Glob(os.DirFS(static), pattern)
+	if err != nil {
+		loadTomlFilesLogger.Error("Failed to glob TOML files for pattern %q: %v", pattern, err)
+		return nil, fmt.Errorf("failed to glob TOML files: %w", err)
+	}
+	loadTomlFilesLogger.Debug("Found %d TOML files for pattern %q", len(tomlFiles), pattern)
+	loadTomlFilesLogger.Trace("TOML files found: %v", tomlFiles)
+
+	for _, tomlFile := range tomlFiles {
+		tomlFile = filepath.Join(static, tomlFile)
+		tomlFile = filepath.Clean(tomlFile)
+		tomlFile = strings.ReplaceAll(tomlFile, "\\", "/")
+		loadTomlFilesLogger.Debug("Loading commands from individual TOML file: %q", tomlFile)
+
+		tomlFileData, err := os.ReadFile(tomlFile)
+		if err != nil {
+			loadTomlFilesLogger.Error("Failed to read TOML file %q: %v", tomlFile, err)
+			return nil, fmt.Errorf("failed to read TOML file: %w", err)
+		}
+		loadTomlFilesLogger.Trace("Read %d bytes from TOML file %q", len(tomlFileData), tomlFile)
+		newCommands, err := LoadCommandsFromTomlFile(tomlFileData)
+		if err != nil {
+			loadTomlFilesLogger.Error("Failed to load commands from TOML file data for %q: %v", tomlFile, err)
+			return nil, fmt.Errorf("failed to load commands from TOML file: %w", err)
+		}
+		commands = append(commands, newCommands...)
+		loadTomlFilesLogger.Debug("Added %d commands from TOML file %q. Total commands now: %d", len(newCommands), tomlFile, len(commands))
+	}
+
+	loadTomlFilesLogger.Debug("Finished loading commands from TOML files. Total %d commands", len(commands))
+	return commands, nil
+}
+
+func LoadCommandsFromTomlFile(tomlFileData []byte) ([]ModifyCommand, error) {
+	loadTomlCommandLogger := modifyCommandLogger.WithPrefix("LoadCommandsFromTomlFile")
+	loadTomlCommandLogger.Debug("Unmarshaling commands from TOML file data")
+	loadTomlCommandLogger.Trace("TOML file data length: %d", len(tomlFileData))
+
+	// TOML structure for commands array
+	var tomlData struct {
+		Commands []ModifyCommand `toml:"commands"`
+		// Also support direct array without wrapper
+		DirectCommands []ModifyCommand `toml:"-"`
+	}
+
+	// First try to parse as wrapped structure
+	err := toml.Unmarshal(tomlFileData, &tomlData)
+	if err != nil {
+		loadTomlCommandLogger.Error("Failed to unmarshal TOML file data: %v", err)
+		return nil, fmt.Errorf("failed to unmarshal TOML file: %w", err)
+	}
+
+	var commands []ModifyCommand
+
+	// If we found commands in the wrapped structure, use those
+	if len(tomlData.Commands) > 0 {
+		commands = tomlData.Commands
+		loadTomlCommandLogger.Debug("Found %d commands in wrapped TOML structure", len(commands))
+	} else {
+		// Try to parse as direct array (similar to YAML format)
+		commands = []ModifyCommand{}
+		err = toml.Unmarshal(tomlFileData, &commands)
+		if err != nil {
+			loadTomlCommandLogger.Error("Failed to unmarshal TOML file data as direct array: %v", err)
+			return nil, fmt.Errorf("failed to unmarshal TOML file as direct array: %w", err)
+		}
+		loadTomlCommandLogger.Debug("Found %d commands in direct TOML array", len(commands))
+	}
+
+	loadTomlCommandLogger.Debug("Successfully unmarshaled %d commands", len(commands))
+	loadTomlCommandLogger.Trace("Unmarshaled commands: %v", commands)
+	return commands, nil
+}
+
+// ConvertYAMLToTOML converts YAML files to TOML format
+func ConvertYAMLToTOML(yamlPattern string) error {
+	convertLogger := modifyCommandLogger.WithPrefix("ConvertYAMLToTOML").WithField("pattern", yamlPattern)
+	convertLogger.Debug("Starting YAML to TOML conversion")
+
+	// Load YAML commands
+	yamlCommands, err := LoadCommandsFromCookFiles(yamlPattern)
+	if err != nil {
+		convertLogger.Error("Failed to load YAML commands: %v", err)
+		return fmt.Errorf("failed to load YAML commands: %w", err)
+	}
+
+	if len(yamlCommands) == 0 {
+		convertLogger.Info("No YAML commands found for pattern: %s", yamlPattern)
+		return nil
+	}
+
+	convertLogger.Debug("Loaded %d commands from YAML", len(yamlCommands))
+
+	// Find all YAML files matching the pattern
+	static, pattern := SplitPattern(yamlPattern)
+	yamlFiles, err := doublestar.Glob(os.DirFS(static), pattern)
+	if err != nil {
+		convertLogger.Error("Failed to glob YAML files: %v", err)
+		return fmt.Errorf("failed to glob YAML files: %w", err)
+	}
+
+	convertLogger.Debug("Found %d YAML files to convert", len(yamlFiles))
+
+	conversionCount := 0
+	skippedCount := 0
+
+	for _, yamlFile := range yamlFiles {
+		yamlFilePath := filepath.Join(static, yamlFile)
+		yamlFilePath = filepath.Clean(yamlFilePath)
+		yamlFilePath = strings.ReplaceAll(yamlFilePath, "\\", "/")
+
+		// Generate corresponding TOML file path
+		tomlFilePath := strings.TrimSuffix(yamlFilePath, filepath.Ext(yamlFilePath)) + ".toml"
+
+		convertLogger.Debug("Processing YAML file: %s -> %s", yamlFilePath, tomlFilePath)
+
+		// Check if TOML file already exists
+		if _, err := os.Stat(tomlFilePath); err == nil {
+			convertLogger.Info("Skipping conversion - TOML file already exists: %s", tomlFilePath)
+			skippedCount++
+			continue
+		}
+
+		// Read YAML file
+		yamlData, err := os.ReadFile(yamlFilePath)
+		if err != nil {
+			convertLogger.Error("Failed to read YAML file %s: %v", yamlFilePath, err)
+			continue
+		}
+
+		// Load YAML commands from this specific file
+		fileCommands, err := LoadCommandsFromCookFile(yamlData)
+		if err != nil {
+			convertLogger.Error("Failed to parse YAML file %s: %v", yamlFilePath, err)
+			continue
+		}
+
+		// Convert to TOML structure
+		tomlData, err := convertCommandsToTOML(fileCommands)
+		if err != nil {
+			convertLogger.Error("Failed to convert commands to TOML for %s: %v", yamlFilePath, err)
+			continue
+		}
+
+		// Write TOML file
+		err = os.WriteFile(tomlFilePath, tomlData, 0644)
+		if err != nil {
+			convertLogger.Error("Failed to write TOML file %s: %v", tomlFilePath, err)
+			continue
+		}
+
+		convertLogger.Info("Successfully converted %s to %s", yamlFilePath, tomlFilePath)
+		conversionCount++
+	}
+
+	convertLogger.Info("Conversion completed: %d files converted, %d files skipped", conversionCount, skippedCount)
+	return nil
+}
+
+// convertCommandsToTOML converts a slice of ModifyCommand to TOML format
+func convertCommandsToTOML(commands []ModifyCommand) ([]byte, error) {
+	convertLogger := modifyCommandLogger.WithPrefix("convertCommandsToTOML")
+	convertLogger.Debug("Converting %d commands to TOML format", len(commands))
+
+	// Create TOML structure
+	tomlData := struct {
+		Commands []ModifyCommand `toml:"commands"`
+	}{
+		Commands: commands,
+	}
+
+	// Marshal to TOML
+	tomlBytes, err := toml.Marshal(tomlData)
+	if err != nil {
+		convertLogger.Error("Failed to marshal commands to TOML: %v", err)
+		return nil, fmt.Errorf("failed to marshal commands to TOML: %w", err)
+	}
+
+	convertLogger.Debug("Successfully converted %d commands to TOML (%d bytes)", len(commands), len(tomlBytes))
+	return tomlBytes, nil
+}