Trim regex to work with yaml pipe

Fuck windows and its path fuck windows

.vscode/launch.json

@@ -12,11 +12,10 @@
 			"program": "${workspaceFolder}",
 			"cwd": "C:/Users/Administrator/Seafile/Games-Barotrauma",
 			"args": [
-				"loglevel",
+				"-loglevel",
 				"trace",
-				"(?-s)LightComponent!anyrange=\"(!num)\"",
+				"-cook",
-				"*4",
+				"*.yml",
-				"**/Outpost*.xml"
 			]
 		},
 		{
@@ -42,9 +41,8 @@
 			"args": [
 				"-loglevel",
 				"trace",
-				"(?-s)LightComponent!anyrange=\"(!num)\"",
+				"-cook",
-				"*4",
+				"cookscoop.yml",
-				"**/Outpost*.xml"
 			]
 		}
 	]

main.go

@@ -4,6 +4,7 @@ import (
 	"flag"
 	"fmt"
 	"os"
+	"sort"
 	"sync"
 	"time"
 
@@ -20,14 +21,14 @@ type GlobalStats struct {
 	TotalModifications      int
 	ProcessedFiles          int
 	FailedFiles             int
-	ModificationsPerCommand map[string]int
+	ModificationsPerCommand sync.Map
 }
 
 var (
 	repo     *git.Repository
 	worktree *git.Worktree
 	stats    GlobalStats = GlobalStats{
-		ModificationsPerCommand: make(map[string]int),
+		ModificationsPerCommand: sync.Map{},
 	}
 )
 
@@ -52,6 +53,7 @@ func main() {
 		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")
 	}
+	// TODO: Fix bed shitting when doing *.yml in barotrauma directory
 	flag.Parse()
 	args := flag.Args()
 
@@ -68,10 +70,27 @@ func main() {
 		return
 	}
 
+	if *utils.Filter != "" {
+		logger.Info("Filtering commands by name: %s", *utils.Filter)
+		commands = utils.FilterCommands(commands, *utils.Filter)
+		logger.Info("Filtered %d commands", len(commands))
+	}
+
 	// Then aggregate all the globs and deduplicate them
 	globs := utils.AggregateGlobs(commands)
 	logger.Debug("Aggregated %d globs before deduplication", utils.CountGlobsBeforeDedup(commands))
 
+	for _, command := range commands {
+		logger.Trace("Command: %s", command.Name)
+		logger.Trace("Regex: %s", command.Regex)
+		logger.Trace("Files: %v", command.Files)
+		logger.Trace("Lua: %s", command.Lua)
+		logger.Trace("Git: %t", command.Git)
+		logger.Trace("Reset: %t", command.Reset)
+		logger.Trace("Isolate: %t", command.Isolate)
+		logger.Trace("LogLevel: %s", command.LogLevel)
+	}
+
 	// Resolve all the files for all the globs
 	logger.Info("Found %d unique file patterns", len(globs))
 	files, err := utils.ExpandGLobs(globs)
@@ -91,7 +110,6 @@ func main() {
 		return
 	}
 
-	// TODO: Utilize parallel workers for this
 	// Then for each file run all commands associated with the file
 	workers := make(chan struct{}, *utils.ParallelFiles)
 	wg := sync.WaitGroup{}
@@ -100,7 +118,34 @@ func main() {
 	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.WithField("command", cmdName)
+		commandLoggers[command.Name].SetLevel(cmdLogLevel)
+
+		logger.Debug("Created logger for command %q with log level %s", cmdName, cmdLogLevel.String())
+	}
+
+	// This aggregation is great but what if one modification replaces the whole entire file?
+	// Shit......
+	// TODO: Add "Isolate" field to modifications which makes them run alone
+	for file, association := range associations {
 		workers <- struct{}{}
 		wg.Add(1)
 		logger.SafeGoWithArgs(func(args ...interface{}) {
@@ -115,39 +160,19 @@ func main() {
 				logger.Error("Failed to read file %q: %v", file, err)
 				return
 			}
-			logger.Trace("Loaded %d bytes of data for file %q", len(fileData), file)
 			fileDataStr := string(fileData)
 
-			// Aggregate all the modifications and execute them
+			fileDataStr, err = RunIsolateCommands(association, file, fileDataStr, &fileMutex)
-			modifications := []utils.ReplaceCommand{}
-			for _, command := range commands {
-				logger.Info("Processing file %q with command %q", file, command.Regex)
-				commands, err := processor.ProcessRegex(fileDataStr, command)
 			if err != nil {
-					logger.Error("Failed to process file %q with command %q: %v", file, command.Regex, err)
+				logger.Error("Failed to run isolate commands for file %q: %v", file, err)
-					return
-				}
-				modifications = append(modifications, commands...)
-				// It is not guranteed that all the commands will be executed...
-				// TODO: Make this better
-				// We'd have to pass the map to executemodifications or something...
-				stats.ModificationsPerCommand[command.Name] += len(commands)
-			}
-
-			if len(modifications) == 0 {
-				logger.Info("No modifications found for file %q", file)
 				return
 			}
 
-			// Sort commands in reverse order for safe replacements
+			fileDataStr, err = RunOtherCommands(file, fileDataStr, association, &fileMutex, commandLoggers)
-			fileDataStr, count := utils.ExecuteModifications(modifications, fileDataStr)
+			if err != nil {
-
+				logger.Error("Failed to run other commands for file %q: %v", file, err)
-			fileMutex.Lock()
+				return
-			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 {
@@ -208,14 +233,95 @@ func main() {
 	// Print summary
 	if stats.TotalModifications == 0 {
 		logger.Warning("No modifications were made in any files")
-		fmt.Fprintf(os.Stderr, "No modifications were made in any files\n")
 	} else {
 		logger.Info("Operation complete! Modified %d values in %d/%d files",
 			stats.TotalModifications, stats.ProcessedFiles, stats.ProcessedFiles+stats.FailedFiles)
-		fmt.Printf("Operation complete! Modified %d values in %d/%d files\n",
+		sortedCommands := []string{}
-			stats.TotalModifications, stats.ProcessedFiles, stats.ProcessedFiles+stats.FailedFiles)
+		stats.ModificationsPerCommand.Range(func(key, value interface{}) bool {
-		for command, count := range stats.ModificationsPerCommand {
+			sortedCommands = append(sortedCommands, key.(string))
-			logger.Info("Command %q made %d modifications", command, count)
+			return true
+		})
+		sort.Strings(sortedCommands)
+
+		for _, command := range sortedCommands {
+			count, _ := stats.ModificationsPerCommand.Load(command)
+			if count.(int) > 0 {
+				logger.Info("\tCommand %q made %d modifications", command, count)
+			} else {
+				logger.Warning("\tCommand %q made no modifications", command)
+			}
 		}
 	}
 }
+
+func RunOtherCommands(file string, fileDataStr string, association utils.FileCommandAssociation, fileMutex *sync.Mutex, commandLoggers map[string]*logger.Logger) (string, error) {
+	// Aggregate all the modifications and execute them
+	modifications := []utils.ReplaceCommand{}
+	for _, command := range association.Commands {
+		// Use command-specific logger if available, otherwise fall back to default logger
+		cmdLogger := logger.DefaultLogger
+		if cmdLog, ok := commandLoggers[command.Name]; ok {
+			cmdLogger = cmdLog
+		}
+
+		cmdLogger.Info("Processing file %q with command %q", file, command.Regex)
+		newModifications, err := processor.ProcessRegex(fileDataStr, command, file)
+		if err != nil {
+			return fileDataStr, fmt.Errorf("failed to process file %q with command %q: %w", file, command.Regex, err)
+		}
+		modifications = append(modifications, newModifications...)
+		// 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(newModifications))
+
+		cmdLogger.Debug("Command %q generated %d modifications", command.Name, len(newModifications))
+	}
+
+	if len(modifications) == 0 {
+		logger.Info("No modifications found for file %q", file)
+		return fileDataStr, nil
+	}
+
+	// Sort commands in reverse order for safe replacements
+	var count int
+	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)
+	return fileDataStr, nil
+}
+
+func RunIsolateCommands(association utils.FileCommandAssociation, file string, fileDataStr string, fileMutex *sync.Mutex) (string, error) {
+	for _, isolateCommand := range association.IsolateCommands {
+		logger.Info("Processing file %q with isolate command %q", file, isolateCommand.Regex)
+		modifications, err := processor.ProcessRegex(fileDataStr, isolateCommand, file)
+		if err != nil {
+			return fileDataStr, fmt.Errorf("failed to process file %q with isolate command %q: %w", file, isolateCommand.Regex, err)
+		}
+
+		if len(modifications) == 0 {
+			logger.Warning("No modifications found for file %q", file)
+			return fileDataStr, nil
+		}
+
+		var count int
+		fileDataStr, count = utils.ExecuteModifications(modifications, fileDataStr)
+
+		fileMutex.Lock()
+		stats.ProcessedFiles++
+		stats.TotalModifications += count
+		fileMutex.Unlock()
+
+		logger.Info("Executed %d isolate modifications for file %q", count, file)
+	}
+	return fileDataStr, nil
+}

processor/regex.go

@@ -21,7 +21,9 @@ 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
+// It's not used for anything else
+func ProcessRegex(content string, command utils.ModifyCommand, filename string) ([]utils.ReplaceCommand, error) {
 	var commands []utils.ReplaceCommand
 	logger.Trace("Processing regex: %q", command.Regex)
 
@@ -31,6 +33,11 @@ func ProcessRegex(content string, command utils.ModifyCommand) ([]utils.ReplaceC
 	// 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)
+	// I'm not too happy about having to trim regex, we could have meaningful whitespace or newlines
+	// But it's a compromise that allows us to use | in yaml
+	// Otherwise we would have to escape every god damn pair of quotation marks
+	// And a bunch of other shit
+	pattern = strings.TrimSpace(pattern)
 	logger.Debug("Compiling regex pattern: %s", pattern)
 
 	patternCompileStart := time.Now()
@@ -79,6 +86,7 @@ func ProcessRegex(content string, command utils.ModifyCommand) ([]utils.ReplaceC
 			logger.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
@@ -153,7 +161,11 @@ func ProcessRegex(content string, command utils.ModifyCommand) ([]utils.ReplaceC
 			}
 		}
 
+		// Use the DeduplicateGroups flag to control whether to deduplicate capture groups
+		if !command.NoDedup {
+			logger.Debug("Deduplicating capture groups as specified in command settings")
 			captureGroups = deduplicateGroups(captureGroups)
+		}
 
 		if err := toLua(L, captureGroups); err != nil {
 			logger.Error("Failed to set Lua variables: %v", err)
@@ -205,7 +217,7 @@ func ProcessRegex(content string, command utils.ModifyCommand) ([]utils.ReplaceC
 
 			for _, capture := range captureGroups {
 				if capture.Value == capture.Updated {
-					logger.Info("Capture group unchanged: %s", capture.Value)
+					logger.Info("Capture group unchanged: %s", LimitString(capture.Value, 50))
 					continue
 				}
 
@@ -250,7 +262,7 @@ func deduplicateGroups(captureGroups []*CaptureGroup) []*CaptureGroup {
 		}
 		if overlaps {
 			// We CAN just continue despite this fuckup
-			logger.Error("Overlapping capture group: %s", group.Name)
+			logger.Warning("Overlapping capture group: %s", group.Name)
 			continue
 		}
 		logger.Debug("No overlap detected for capture group: %s. Adding to deduplicated groups.", group.Name)
@@ -268,8 +280,6 @@ func resolveRegexPlaceholders(pattern string) string {
 	// Handle special pattern modifications
 	if !strings.HasPrefix(pattern, "(?s)") {
 		pattern = "(?s)" + pattern
-		// Use fmt.Printf for test compatibility
-		fmt.Printf("Pattern modified to include (?s): %s\n", pattern)
 	}
 
 	namedGroupNum := regexp.MustCompile(`(?:(\?<[^>]+>)(!num))`)

processor/regex_test.go

@@ -2,7 +2,6 @@ package processor
 
 import (
 	"bytes"
-	"fmt"
 	"io"
 	"modify/utils"
 	"os"
@@ -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
 	}
@@ -979,29 +978,12 @@ func TestPatternWithoutPrefixGetsModified(t *testing.T) {
 	// Setup
 	pattern := "some.*pattern"
 
-	// Redirect stdout to capture fmt.Printf output
-	oldStdout := os.Stdout
-	r, w, _ := os.Pipe()
-	os.Stdout = w
-
 	// Execute function
 	result := resolveRegexPlaceholders(pattern)
 
-	// Restore stdout
-	w.Close()
-	os.Stdout = oldStdout
-
-	// Read captured output
-	var buf bytes.Buffer
-	io.Copy(&buf, r)
-	output := buf.String()
-
 	// Verify results
 	expectedPattern := "(?s)some.*pattern"
 	assert.Equal(t, expectedPattern, result, "Expected pattern to be %q, got %q", expectedPattern, result)
-
-	expectedOutput := fmt.Sprintf("Pattern modified to include (?s): %s\n", expectedPattern)
-	assert.Equal(t, expectedOutput, output, "Expected output message %q, got %q", expectedOutput, output)
 }
 
 // Empty string input returns "(?s)"
@@ -1009,29 +991,12 @@ func TestEmptyStringReturnsWithPrefix(t *testing.T) {
 	// Setup
 	pattern := ""
 
-	// Redirect stdout to capture fmt.Printf output
-	oldStdout := os.Stdout
-	r, w, _ := os.Pipe()
-	os.Stdout = w
-
 	// Execute function
 	result := resolveRegexPlaceholders(pattern)
 
-	// Restore stdout
-	w.Close()
-	os.Stdout = oldStdout
-
-	// Read captured output
-	var buf bytes.Buffer
-	io.Copy(&buf, r)
-	output := buf.String()
-
 	// Verify results
 	expectedPattern := "(?s)"
 	assert.Equal(t, expectedPattern, result, "Expected pattern to be %q, got %q", expectedPattern, result)
-
-	expectedOutput := fmt.Sprintf("Pattern modified to include (?s): %s\n", expectedPattern)
-	assert.Equal(t, expectedOutput, output, "Expected output message %q, got %q", expectedOutput, output)
 }
 
 // Named group with "!num" pattern gets replaced with proper regex for numbers

regression/regression_test.go

@@ -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/flags.go

@@ -12,4 +12,5 @@ var (
 	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")
 )

utils/modifycommand.go

@@ -4,6 +4,8 @@ import (
 	"fmt"
 	"modify/logger"
 	"os"
+	"path/filepath"
+	"strings"
 
 	"github.com/bmatcuk/doublestar/v4"
 	"gopkg.in/yaml.v3"
@@ -17,6 +19,8 @@ type ModifyCommand struct {
 	Git      bool     `yaml:"git"`
 	Reset    bool     `yaml:"reset"`
 	LogLevel string   `yaml:"loglevel"`
+	Isolate  bool     `yaml:"isolate"`
+	NoDedup  bool     `yaml:"nodedup"`
 }
 type CookFile []ModifyCommand
 
@@ -36,29 +40,75 @@ func (c *ModifyCommand) Validate() error {
 	return nil
 }
 
-func AssociateFilesWithCommands(files []string, commands []ModifyCommand) (map[string][]ModifyCommand, error) {
+// Ehh.. Not much better... Guess this wasn't the big deal
+var matchesMemoTable map[string]bool = make(map[string]bool)
+
+func Matches(path string, glob string) (bool, error) {
+	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)
+		return matches, nil
+	}
+	matches, err := doublestar.Match(glob, path)
+	if err != nil {
+		return false, fmt.Errorf("failed to match glob %s with file %s: %w", glob, path, err)
+	}
+	matchesMemoTable[key] = matches
+	return matches, nil
+}
+
+type FileCommandAssociation struct {
+	File            string
+	IsolateCommands []ModifyCommand
+	Commands        []ModifyCommand
+}
+
+func AssociateFilesWithCommands(files []string, commands []ModifyCommand) (map[string]FileCommandAssociation, error) {
 	associationCount := 0
-	fileCommands := make(map[string][]ModifyCommand)
+	fileCommands := make(map[string]FileCommandAssociation)
+
 	for _, file := range files {
+		fileCommands[file] = FileCommandAssociation{
+			File:            file,
+			IsolateCommands: []ModifyCommand{},
+			Commands:        []ModifyCommand{},
+		}
 		for _, command := range commands {
 			for _, glob := range command.Files {
-				// TODO: Maybe memoize this function call
+				_, pattern, err := FigureOutGlobRoot(glob)
-				matches, err := doublestar.Match(glob, file)
+				if err != nil {
+					logger.Trace("Failed to figure out glob root for %s: %v", glob, err)
+					continue
+				}
+				file = filepath.Clean(file)
+				file = strings.ReplaceAll(file, "\\", "/")
+
+				matches, err := Matches(file, pattern)
 				if err != nil {
 					logger.Trace("Failed to match glob %s with file %s: %v", glob, file, err)
 					continue
 				}
 				if matches {
 					logger.Debug("Found match for file %q and command %q", file, command.Regex)
-					fileCommands[file] = append(fileCommands[file], command)
+					association := fileCommands[file]
+
+					if command.Isolate {
+						association.IsolateCommands = append(association.IsolateCommands, command)
+					} else {
+						association.Commands = append(association.Commands, command)
+					}
+					fileCommands[file] = association
 					associationCount++
 				}
 			}
 		}
-		logger.Debug("Found %d commands for file %q", len(fileCommands[file]), file)
+		logger.Debug("Found %d commands for file %q", len(fileCommands[file].Commands), file)
-		if len(fileCommands[file]) == 0 {
+		if len(fileCommands[file].Commands) == 0 {
 			logger.Info("No commands found for file %q", file)
 		}
+		if len(fileCommands[file].IsolateCommands) > 0 {
+			logger.Info("Found %d isolate commands for file %q", len(fileCommands[file].IsolateCommands), file)
+		}
 	}
 	logger.Info("Found %d associations between %d files and %d commands", associationCount, len(files), len(commands))
 	return fileCommands, nil
@@ -69,6 +119,8 @@ func AggregateGlobs(commands []ModifyCommand) map[string]struct{} {
 	globs := make(map[string]struct{})
 	for _, command := range commands {
 		for _, glob := range command.Files {
+			glob = strings.ReplaceAll(glob, "~", os.Getenv("USERPROFILE"))
+			glob = strings.ReplaceAll(glob, "\\", "/")
 			globs[glob] = struct{}{}
 		}
 	}
@@ -76,21 +128,87 @@ func AggregateGlobs(commands []ModifyCommand) map[string]struct{} {
 	return globs
 }
 
+func FigureOutGlobRoot(inputPattern string) (root, pattern string, err error) {
+	logger.Debug("Starting to figure out glob root for input pattern: %s", inputPattern)
+
+	cwd, err := os.Getwd()
+	if err != nil {
+		logger.Error("Failed to get current working directory: %v", err)
+		return "", inputPattern, fmt.Errorf("failed to get current working directory: %w", err)
+	}
+	logger.Trace("Current working directory: %s", cwd)
+
+	root = inputPattern
+	if !filepath.IsAbs(inputPattern) {
+		root = filepath.Join(cwd, inputPattern)
+		logger.Info("Input pattern is not absolute. Using combined path: %s", root)
+	}
+	root = filepath.Clean(root)
+	logger.Debug("Cleaned root path: %s", root)
+
+	// In either case (whatever our root may be), we have to figure out
+	// Where to start, what our FS will be
+	// The best place would be the last sure entry
+	// That is to say the final directory that is not a wildcard
+
+	finalroot := ""
+	// TODO: This will probably explode on linux because oooooooooo we have to be clever oooooooooo / on linux \\ on windows ooooooooooo
+	parts := strings.Split(root, "\\")
+	lastIndex := len(parts) - 1
+	logger.Debug("Split root into parts: %v", parts)
+
+	// In the case our pattern ends with a file (and many of them do)
+	// Look for only the folders, we cannot mount a file as a FS
+	// In any case we have to match files so they have to be the last part
+	for i := 0; i < len(parts)-1; i++ {
+		part := parts[i]
+		logger.Trace("Processing part: %s", part)
+		if part == "*" || part == "**" || part == "?" || part == "[" {
+			lastIndex = i
+			logger.Debug("Found wildcard part: %s, updating lastIndex to: %d", part, lastIndex)
+			break
+		}
+		// We can't use join here because it joins C: and Users as C:Users
+		// Instead of C:/Users/
+		// God damn it
+		if finalroot != "" {
+			finalroot = finalroot + "/" + part
+		} else {
+			finalroot = finalroot + part
+		}
+	}
+	finalroot = filepath.Clean(finalroot)
+	logger.Debug("Final root after processing: %s", finalroot)
+
+	// After all this juggling our pattern is whatever is left after the finalroot
+	// Which is, in "worst" case, only a file
+	pattern = strings.Join(parts[lastIndex:], "/")
+	logger.Info("Determined pattern: %s", pattern)
+
+	return finalroot, pattern, nil
+}
+
 func ExpandGLobs(patterns map[string]struct{}) ([]string, error) {
 	var files []string
 	filesMap := make(map[string]bool)
 
-	cwd, err := os.Getwd()
+	for pattern := range patterns {
+		root, pattern, err := FigureOutGlobRoot(pattern)
 		if err != nil {
-		return nil, fmt.Errorf("failed to get current working directory: %w", err)
+			return nil, fmt.Errorf("failed to figure out glob root: %w", err)
 		}
 
-	logger.Debug("Expanding patterns from directory: %s", cwd)
-	for pattern := range patterns {
 		logger.Trace("Processing pattern: %s", pattern)
-		matches, _ := doublestar.Glob(os.DirFS(cwd), pattern)
+		matches, err := doublestar.Glob(os.DirFS(root), pattern)
+		if err != nil {
+			return nil, fmt.Errorf("failed to glob pattern %s: %w", pattern, err)
+		}
 		logger.Debug("Found %d matches for pattern %s", len(matches), pattern)
 		for _, m := range matches {
+			m = filepath.Join(root, m)
+			m = filepath.Clean(m)
+			m = strings.ReplaceAll(m, "\\", "/")
+
 			info, err := os.Stat(m)
 			if err != nil {
 				logger.Warning("Error getting file info for %s: %v", m, err)
@@ -206,3 +324,16 @@ func CountGlobsBeforeDedup(commands []ModifyCommand) int {
 	}
 	return count
 }
+
+func FilterCommands(commands []ModifyCommand, filter string) []ModifyCommand {
+	filteredCommands := []ModifyCommand{}
+	filters := strings.Split(filter, ",")
+	for _, cmd := range commands {
+		for _, filter := range filters {
+			if strings.Contains(cmd.Name, filter) {
+				filteredCommands = append(filteredCommands, cmd)
+			}
+		}
+	}
+	return filteredCommands
+}

utils/modifycommand_test.go

@@ -3,6 +3,7 @@ package utils
 import (
 	"os"
 	"path/filepath"
+	"strings"
 	"testing"
 
 	"github.com/stretchr/testify/assert"
@@ -158,21 +159,24 @@ 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 +191,12 @@ 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 +211,12 @@ 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++
@@ -393,10 +397,10 @@ 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 +424,11 @@ 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 +449,7 @@ 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 +500,13 @@ 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
 `)
 
@@ -1266,3 +1270,164 @@ func TestLoadCommandsFromCookFilesNoYamlFiles(t *testing.T) {
 // 		t.Errorf("Expected 0 commands, got: %d", len(commands))
 // 	}
 // }
+
+// Absolute path without wildcards returns correct root and pattern
+func TestFigureOutGlobRootWithAbsolutePathNoWildcards(t *testing.T) {
+	// Setup
+	absPath := filepath.Join("C:\\Users", "test", "documents", "file.txt")
+
+	// Execute
+	root, pattern, err := FigureOutGlobRoot(absPath)
+
+	// Assert
+	assert.NoError(t, err)
+	expectedRoot := filepath.Clean(filepath.Join("C:\\Users", "test", "documents"))
+	assert.Equal(t, expectedRoot, root)
+	assert.Equal(t, "file.txt", pattern)
+}
+
+// Empty input pattern handling - we expect our "Patter", such as it is, to be a folder
+func TestFigureOutGlobRootWithEmptyPattern(t *testing.T) {
+	// Setup
+	emptyPattern := ""
+
+	// Execute
+	root, pattern, err := FigureOutGlobRoot(emptyPattern)
+
+	// Assert
+	assert.NoError(t, err)
+	cwd, _ := os.Getwd()
+	cwdParts := strings.Split(filepath.Clean(cwd), "\\")
+	expectedRoot := strings.Join(cwdParts[:len(cwdParts)-1], "\\")
+	expectedPattern := cwdParts[len(cwdParts)-1]
+	assert.Equal(t, expectedRoot, root)
+	assert.Equal(t, expectedPattern, pattern)
+}
+
+// Relative path is correctly joined with current working directory
+func TestFigureOutGlobRootWithRelativePath(t *testing.T) {
+	// Setup
+	cwd, err := os.Getwd()
+	assert.NoError(t, err)
+	relPath := "test/documents/file.txt"
+
+	// Execute
+	root, pattern, err := FigureOutGlobRoot(relPath)
+
+	// Assert
+	assert.NoError(t, err)
+	expectedRoot := filepath.Clean(filepath.Join(cwd, "test/documents"))
+	assert.Equal(t, expectedRoot, root)
+	assert.Equal(t, "file.txt", pattern)
+}
+
+// Path with wildcards correctly identifies the last non-wildcard directory as root
+func TestFigureOutGlobRootWithWildcards(t *testing.T) {
+	// Setup
+	inputPattern := filepath.Join("C:\\Users", "test", "documents", "*", "file.txt")
+
+	// Execute
+	root, pattern, err := FigureOutGlobRoot(inputPattern)
+
+	// Assert
+	assert.NoError(t, err)
+	expectedRoot := filepath.Clean(filepath.Join("C:\\Users", "test", "documents"))
+	assert.Equal(t, expectedRoot, root)
+	assert.Equal(t, "*/file.txt", pattern)
+}
+
+// Windows-style paths are properly handled and converted
+func TestFigureOutGlobRootWithRelativePathAndWildcards(t *testing.T) {
+	// Setup
+	inputPattern := "documents\\*\\file?.txt"
+	cwd, _ := os.Getwd()
+
+	// Execute
+	root, pattern, err := FigureOutGlobRoot(inputPattern)
+
+	// Assert
+	assert.NoError(t, err)
+	expectedRoot := filepath.Clean(filepath.Join(cwd, "documents"))
+	assert.Equal(t, expectedRoot, root)
+	assert.Equal(t, "*/file?.txt", pattern)
+}
+
+// Path with only wildcards (e.g., "*" or "**")
+func TestFigureOutGlobRootWithOnlyWildcards(t *testing.T) {
+	// Setup
+	wildcardPattern := "*"
+
+	// Execute
+	root, pattern, err := FigureOutGlobRoot(wildcardPattern)
+
+	// Assert
+	assert.NoError(t, err)
+	expectedRoot, _ := os.Getwd()
+	assert.Equal(t, expectedRoot, root)
+	assert.Equal(t, "*", pattern)
+}
+
+// Multiple path segments are correctly processed and joined
+func TestFigureOutGlobRootWithRelativePathAndWildcards2(t *testing.T) {
+	// Setup
+	cwd, err := os.Getwd()
+	assert.NoError(t, err)
+	relPath := filepath.Join("test", "data", "*", "file?.txt")
+
+	// Execute
+	root, pattern, err := FigureOutGlobRoot(relPath)
+
+	// Assert
+	assert.NoError(t, err)
+	expectedRoot := filepath.Clean(filepath.Join(cwd, "test", "data"))
+	assert.Equal(t, expectedRoot, root)
+	assert.Equal(t, "*/file?.txt", pattern)
+}
+
+// Path with mixed forward and backward slashes
+func TestFigureOutGlobRootWithMixedSlashes(t *testing.T) {
+	// Setup
+	mixedPath := "C:\\Users/test\\documents\\file.txt"
+
+	// Execute
+	root, pattern, err := FigureOutGlobRoot(mixedPath)
+
+	// Assert
+	assert.NoError(t, err)
+	expectedRoot := filepath.Clean(filepath.Join("C:\\Users", "test", "documents"))
+	assert.Equal(t, expectedRoot, root)
+	assert.Equal(t, "file.txt", pattern)
+}
+
+// Path with wildcards in the first segment
+func TestFigureOutGlobRootWithWildcardInFirstSegment(t *testing.T) {
+	// Setup
+	inputPattern := "*\\Users\\test\\documents\\file.txt"
+	cwd, _ := os.Getwd()
+
+	// Execute
+	root, pattern, err := FigureOutGlobRoot(inputPattern)
+
+	// Assert
+	assert.NoError(t, err)
+	expectedRoot := filepath.Clean(cwd)
+	assert.Equal(t, expectedRoot, root)
+	assert.Equal(t, "*/Users/test/documents/file.txt", pattern)
+}
+
+// Handling of relative paths with ".." or "." components
+func TestFigureOutGlobRootWithRelativePathAndDotComponents(t *testing.T) {
+	// Setup
+	cwd, err := os.Getwd()
+	assert.NoError(t, err)
+	relPath := filepath.Join("..", ".", "test", "documents", "file.txt")
+
+	// Execute
+	root, pattern, err := FigureOutGlobRoot(relPath)
+
+	// Assert
+	assert.NoError(t, err)
+	expectedRoot := filepath.Clean(filepath.Join(cwd, "..", "test", "documents"))
+	assert.Equal(t, expectedRoot, root)
+	assert.Equal(t, "file.txt", pattern)
+}