fix: critical hooks bug - preserve all Claude Code settings

BREAKING BUG FIX: Hook installation was destroying existing Claude Code settings

- Fix critical data loss in --install-hook and --uninstall-hook commands
- Change ClaudeSettings to preserve ALL existing JSON settings via Data map
- Add automatic timestamped backup creation before any settings modification
- Implement surgical hook installation that adds to existing config structure
- Implement surgical hook removal that only removes shush hooks
- Prevent loss of user settings like includeCoAuthoredBy, themes, etc.
- Add comprehensive error handling for malformed settings files

This was a critical data loss bug that could destroy users' Claude Code configurations.
All existing settings are now preserved during hook operations.

Fixes: Users losing their Claude Code settings during hook installation
Added: Automatic backups with timestamp (settings.json.backup.TIMESTAMP)
Improved: Hook management now respects existing PostToolUse configurations

README.md

@@ -17,6 +17,24 @@ Download the binary for your platform from the [releases page](https://github.co
 
 ## Usage
 
+### 🤖 Claude Code Integration (Most Popular!)
+
+```bash
+# Install automatic comment cleanup after Claude modifies files
+shush --install-hook              # User-wide (all projects)
+shush --install-hook -s project   # Project-specific only
+
+# Manage hooks
+shush --hook-status               # Check installation status
+shush --list-hooks                # Show all configured hooks
+shush --uninstall-hook            # Remove hooks
+
+# Once installed, comments are automatically cleaned whenever Claude Code 
+# uses Write, Edit, or MultiEdit tools! Respects your .shush.toml config.
+```
+
+### 📂 Basic File Operations
+
 ```bash
 # Remove all comments from a file
 shush file.py
@@ -44,18 +62,23 @@ shush script.py --preserve-lines
 
 # Verbose output
 shush app.go --verbose
+```
 
+### 🔀 Git-Aware Processing
+
+```bash
 # Git-aware processing (only process changed lines)
 shush --staged                    # Clean comments from staged changes
 shush --unstaged                  # Clean comments from unstaged changes  
 shush --changes-only              # Clean comments from all changes
+```
 
-# Configuration and hooks management
+### ⚙️ Configuration Management
+
+```bash
+# Configuration management
 shush --create-config             # Create .shush.toml configuration
 shush --config                    # Show current configuration
-shush --install-hook              # Install Claude Code hooks (user-wide)
-shush --install-hook -s project   # Install project-specific hooks
-shush --hook-status               # Check hook installation status
 
 # Combine flags for complex operations
 shush src/ --recursive --inline --dry-run --verbose

cmd/shush/main.go

@@ -12,7 +12,7 @@ import (
 	"github.com/carlosarraes/shush/internal/types"
 )
 
-var version = "0.2.2"
+var version = "0.2.3"
 
 func main() {
 	var cliArgs types.CLI

internal/commands/hooks.go

@@ -62,6 +62,10 @@ func InstallHooks(scope string) error {
 		return fmt.Errorf("failed to get settings path: %w", err)
 	}
 
+	if err := hooks.CreateBackup(path); err != nil {
+		return fmt.Errorf("failed to create backup: %w", err)
+	}
+
 	settings, err := hooks.LoadSettings(path)
 	if err != nil {
 		return fmt.Errorf("failed to load settings: %w", err)
@@ -109,6 +113,10 @@ func UninstallHooks(scope string) error {
 		return fmt.Errorf("shush hook not found for %s scope at %s", scopeName, path)
 	}
 
+	if err := hooks.CreateBackup(path); err != nil {
+		return fmt.Errorf("failed to create backup: %w", err)
+	}
+
 	if _, err := exec.LookPath("jq"); err == nil {
 		if err := uninstallWithJQ(path, scopeName); err == nil {
 			return nil
@@ -222,19 +230,56 @@ func listHooksForPath(path string) error {
 		return err
 	}
 
-	if len(settings.Hooks) == 0 {
+	hooksData, exists := settings.Data["hooks"]
+	if !exists {
+		return fmt.Errorf("no hooks")
+	}
+
+	hooksMap, ok := hooksData.(map[string]interface{})
+	if !ok {
+		return fmt.Errorf("invalid hooks format")
+	}
+
+	if len(hooksMap) == 0 {
 		return fmt.Errorf("no hooks")
 	}
 
 	hasShush := hooks.HasShushHook(settings)
 
-	for event, configs := range settings.Hooks {
-		for _, config := range configs {
-			for _, hook := range config.Hooks {
-				if hook.Command == "shush --changes-only" {
-					fmt.Printf("  ✓ shush --changes-only (%s: %s)\n", event, config.Matcher)
+	for event, eventData := range hooksMap {
+		configs, ok := eventData.([]interface{})
+		if !ok {
+			continue
+		}
+
+		for _, configData := range configs {
+			config, ok := configData.(map[string]interface{})
+			if !ok {
+				continue
+			}
+
+			matcher, _ := config["matcher"].(string)
+			hooksData, exists := config["hooks"]
+			if !exists {
+				continue
+			}
+
+			hooks, ok := hooksData.([]interface{})
+			if !ok {
+				continue
+			}
+
+			for _, hookData := range hooks {
+				hook, ok := hookData.(map[string]interface{})
+				if !ok {
+					continue
+				}
+
+				command, _ := hook["command"].(string)
+				if command == "shush --changes-only" {
+					fmt.Printf("  ✓ shush --changes-only (%s: %s)\n", event, matcher)
 				} else {
-					fmt.Printf("  ✓ %s (%s: %s)\n", hook.Command, event, config.Matcher)
+					fmt.Printf("  ✓ %s (%s: %s)\n", command, event, matcher)
 				}
 			}
 		}

internal/hooks/hooks.go

@@ -7,6 +7,7 @@ import (
 	"os"
 	"path/filepath"
 	"strings"
+	"time"
 )
 
 type HookScope int
@@ -17,7 +18,7 @@ const (
 )
 
 type ClaudeSettings struct {
-	Hooks map[string][]EventConfig `json:"hooks,omitempty"`
+	Data map[string]interface{} `json:"-"`
 }
 
 type EventConfig struct {
@@ -58,28 +59,50 @@ func EnsureSettingsDirectory(settingsPath string) error {
 	return nil
 }
 
+func CreateBackup(settingsPath string) error {
+	if _, err := os.Stat(settingsPath); os.IsNotExist(err) {
+		return nil
+	}
+
+	timestamp := time.Now().Unix()
+	backupPath := fmt.Sprintf("%s.backup.%d", settingsPath, timestamp)
+
+	data, err := os.ReadFile(settingsPath)
+	if err != nil {
+		return fmt.Errorf("failed to read original settings for backup: %w", err)
+	}
+
+	if err := os.WriteFile(backupPath, data, 0644); err != nil {
+		return fmt.Errorf("failed to create backup at %s: %w", backupPath, err)
+	}
+
+	fmt.Printf("✓ Backup created: %s\n", backupPath)
+	return nil
+}
+
 func LoadSettings(path string) (*ClaudeSettings, error) {
 	data, err := os.ReadFile(path)
 	if err != nil {
 		if os.IsNotExist(err) {
-
 			return &ClaudeSettings{
-				Hooks: make(map[string][]EventConfig),
+				Data: make(map[string]interface{}),
 			}, nil
 		}
 		return nil, fmt.Errorf("failed to read settings file %s: %w", path, err)
 	}
 
-	var settings ClaudeSettings
-	if err := json.Unmarshal(data, &settings); err != nil {
+	var allSettings map[string]interface{}
+	if err := json.Unmarshal(data, &allSettings); err != nil {
 		return nil, fmt.Errorf("failed to parse settings file %s: %w", path, err)
 	}
 
-	if settings.Hooks == nil {
-		settings.Hooks = make(map[string][]EventConfig)
+	if allSettings == nil {
+		allSettings = make(map[string]interface{})
 	}
 
-	return &settings, nil
+	return &ClaudeSettings{
+		Data: allSettings,
+	}, nil
 }
 
 func SaveSettings(path string, settings *ClaudeSettings) error {
@@ -87,7 +110,7 @@ func SaveSettings(path string, settings *ClaudeSettings) error {
 		return err
 	}
 
-	data, err := json.MarshalIndent(settings, "", "  ")
+	data, err := json.MarshalIndent(settings.Data, "", "  ")
 	if err != nil {
 		return fmt.Errorf("failed to marshal settings: %w", err)
 	}
@@ -115,18 +138,55 @@ func CreateShushEventConfig() EventConfig {
 }
 
 func HasShushHook(settings *ClaudeSettings) bool {
-	if settings.Hooks == nil {
-		return false
-	}
-
-	postToolUseConfigs, exists := settings.Hooks["PostToolUse"]
+	hooksData, exists := settings.Data["hooks"]
 	if !exists {
 		return false
 	}
 
-	for _, config := range postToolUseConfigs {
-		for _, hook := range config.Hooks {
-			if strings.Contains(hook.Command, "shush --changes-only") {
+	hooksMap, ok := hooksData.(map[string]interface{})
+	if !ok {
+		return false
+	}
+
+	postToolUseData, exists := hooksMap["PostToolUse"]
+	if !exists {
+		return false
+	}
+
+	postToolUseConfigs, ok := postToolUseData.([]interface{})
+	if !ok {
+		return false
+	}
+
+	for _, configData := range postToolUseConfigs {
+		config, ok := configData.(map[string]interface{})
+		if !ok {
+			continue
+		}
+
+		hooksData, exists := config["hooks"]
+		if !exists {
+			continue
+		}
+
+		hooks, ok := hooksData.([]interface{})
+		if !ok {
+			continue
+		}
+
+		for _, hookData := range hooks {
+			hook, ok := hookData.(map[string]interface{})
+			if !ok {
+				continue
+			}
+
+			command, exists := hook["command"]
+			if !exists {
+				continue
+			}
+
+			commandStr, ok := command.(string)
+			if ok && strings.Contains(commandStr, "shush --changes-only") {
 				return true
 			}
 		}
@@ -136,71 +196,175 @@ func HasShushHook(settings *ClaudeSettings) bool {
 }
 
 func AddShushHook(settings *ClaudeSettings) error {
-	if settings.Hooks == nil {
-		settings.Hooks = make(map[string][]EventConfig)
-	}
-
 	if HasShushHook(settings) {
 		return errors.New("shush hook already installed")
 	}
 
-	postToolUseConfigs, exists := settings.Hooks["PostToolUse"]
-	if !exists {
+	if _, exists := settings.Data["hooks"]; !exists {
+		settings.Data["hooks"] = make(map[string]interface{})
+	}
 
-		settings.Hooks["PostToolUse"] = []EventConfig{CreateShushEventConfig()}
+	hooksMap := settings.Data["hooks"].(map[string]interface{})
+
+	shushHook := map[string]interface{}{
+		"type":    "command",
+		"command": "shush --changes-only",
+		"timeout": 30,
+	}
+
+	if postToolUseData, exists := hooksMap["PostToolUse"]; exists {
+		postToolUseConfigs, ok := postToolUseData.([]interface{})
+		if !ok {
+			return errors.New("invalid PostToolUse format in existing settings")
+		}
+
+		for _, configData := range postToolUseConfigs {
+			config, ok := configData.(map[string]interface{})
+			if !ok {
+				continue
+			}
+
+			matcher, exists := config["matcher"]
+			if !exists {
+				continue
+			}
+
+			matcherStr, ok := matcher.(string)
+			if !ok {
+				continue
+			}
+
+			if matcherStr == "Write|Edit|MultiEdit" {
+				hooksData, exists := config["hooks"]
+				if !exists {
+					config["hooks"] = []interface{}{shushHook}
+					return nil
+				}
+
+				hooks, ok := hooksData.([]interface{})
+				if !ok {
+					return errors.New("invalid hooks format in existing settings")
+				}
+
+				config["hooks"] = append(hooks, shushHook)
+				return nil
+			}
+		}
+
+		newConfig := map[string]interface{}{
+			"matcher": "Write|Edit|MultiEdit",
+			"hooks":   []interface{}{shushHook},
+		}
+
+		hooksMap["PostToolUse"] = append(postToolUseConfigs, newConfig)
 		return nil
 	}
 
-	for i, config := range postToolUseConfigs {
-		if config.Matcher == "Write|Edit|MultiEdit" || config.Matcher == "" {
-
-			postToolUseConfigs[i].Hooks = append(config.Hooks, CreateShushHookEntry())
-			return nil
-		}
+	newConfig := map[string]interface{}{
+		"matcher": "Write|Edit|MultiEdit",
+		"hooks":   []interface{}{shushHook},
 	}
 
-	settings.Hooks["PostToolUse"] = append(postToolUseConfigs, CreateShushEventConfig())
+	hooksMap["PostToolUse"] = []interface{}{newConfig}
 	return nil
 }
 
 func RemoveShushHook(settings *ClaudeSettings) error {
-	if settings.Hooks == nil {
-		return errors.New("no hooks configuration found")
-	}
-
-	postToolUseConfigs, exists := settings.Hooks["PostToolUse"]
-	if !exists {
+	if !HasShushHook(settings) {
 		return errors.New("shush hook not found")
 	}
 
+	hooksData, exists := settings.Data["hooks"]
+	if !exists {
+		return errors.New("no hooks configuration found")
+	}
+
+	hooksMap, ok := hooksData.(map[string]interface{})
+	if !ok {
+		return errors.New("invalid hooks format")
+	}
+
+	postToolUseData, exists := hooksMap["PostToolUse"]
+	if !exists {
+		return errors.New("no PostToolUse hooks found")
+	}
+
+	postToolUseConfigs, ok := postToolUseData.([]interface{})
+	if !ok {
+		return errors.New("invalid PostToolUse format")
+	}
+
 	found := false
-	for i, config := range postToolUseConfigs {
-		newHooks := make([]HookEntry, 0, len(config.Hooks))
-		for _, hook := range config.Hooks {
-			if !strings.Contains(hook.Command, "shush --changes-only") {
-				newHooks = append(newHooks, hook)
-			} else {
+	var newConfigs []interface{}
+
+	for _, configData := range postToolUseConfigs {
+		config, ok := configData.(map[string]interface{})
+		if !ok {
+			newConfigs = append(newConfigs, configData)
+			continue
+		}
+
+		hooksData, exists := config["hooks"]
+		if !exists {
+			newConfigs = append(newConfigs, configData)
+			continue
+		}
+
+		hooks, ok := hooksData.([]interface{})
+		if !ok {
+			newConfigs = append(newConfigs, configData)
+			continue
+		}
+
+		var newHooks []interface{}
+		for _, hookData := range hooks {
+			hook, ok := hookData.(map[string]interface{})
+			if !ok {
+				newHooks = append(newHooks, hookData)
+				continue
+			}
+
+			command, exists := hook["command"]
+			if !exists {
+				newHooks = append(newHooks, hookData)
+				continue
+			}
+
+			commandStr, ok := command.(string)
+			if !ok {
+				newHooks = append(newHooks, hookData)
+				continue
+			}
+
+			if strings.Contains(commandStr, "shush --changes-only") {
 				found = true
+			} else {
+				newHooks = append(newHooks, hookData)
 			}
 		}
-		postToolUseConfigs[i].Hooks = newHooks
+
+		if len(newHooks) > 0 {
+			newConfig := make(map[string]interface{})
+			for k, v := range config {
+				newConfig[k] = v
+			}
+			newConfig["hooks"] = newHooks
+			newConfigs = append(newConfigs, newConfig)
+		}
 	}
 
 	if !found {
 		return errors.New("shush hook not found")
 	}
 
-	filteredConfigs := make([]EventConfig, 0, len(postToolUseConfigs))
-	for _, config := range postToolUseConfigs {
-		if len(config.Hooks) > 0 {
-			filteredConfigs = append(filteredConfigs, config)
-		}
+	if len(newConfigs) == 0 {
+		delete(hooksMap, "PostToolUse")
+	} else {
+		hooksMap["PostToolUse"] = newConfigs
 	}
 
-	if len(filteredConfigs) == 0 {
-		delete(settings.Hooks, "PostToolUse")
-	} else {
-		settings.Hooks["PostToolUse"] = filteredConfigs
+	if len(hooksMap) == 0 {
+		delete(settings.Data, "hooks")
 	}
 
 	return nil