Fix git hooks not working in worktrees (#1126)

Git hooks are shared across all worktrees and live in the common git
directory (e.g., /repo/.git/hooks), not the worktree-specific directory
(e.g., /repo/.git/worktrees/feature/hooks).

The core issue was in GetGitHooksDir() which used GetGitDir() instead
of GetGitCommonDir(). This caused hooks to be installed to/read from
the wrong location when running in a worktree.

Additionally, several places in the codebase manually constructed
hooks paths using gitDir + "hooks" instead of calling GetGitHooksDir().
These have been updated to use the proper worktree-aware path.

Affected areas:
- GetGitHooksDir() now uses GetGitCommonDir()
- CheckGitHooks() uses GetGitHooksDir()
- installHooks/uninstallHooks use GetGitHooksDir()
- runChainedHook() uses GetGitHooksDir()
- Doctor checks use git-common-dir for hooks paths
- Reset command uses GetGitCommonDir() for hooks and beads-worktrees

Symptoms that this fixes:
- Chained hooks (pre-commit.old) not running in worktrees
- bd hooks install not finding/installing hooks correctly in worktrees
- bd hooks list showing incorrect status in worktrees
- bd doctor reporting incorrect hooks status in worktrees

Co-authored-by: Zain Rizvi <4468967+ZainRizvi@users.noreply.github.com>

cmd/bd/doctor/fix/hooks.go

@@ -108,20 +108,20 @@ var hookManagerPatterns = []hookManagerPattern{
 // DetectActiveHookManager reads the git hooks to determine which manager installed them.
 // This is more reliable than just checking for config files when multiple managers exist.
 func DetectActiveHookManager(path string) string {
-	// Get git dir
-	cmd := exec.Command("git", "rev-parse", "--git-dir")
+	// Get common git dir (hooks are shared across worktrees)
+	cmd := exec.Command("git", "rev-parse", "--git-common-dir")
 	cmd.Dir = path
 	output, err := cmd.Output()
 	if err != nil {
 		return ""
 	}
-	gitDir := strings.TrimSpace(string(output))
-	if !filepath.IsAbs(gitDir) {
-		gitDir = filepath.Join(path, gitDir)
+	gitCommonDir := strings.TrimSpace(string(output))
+	if !filepath.IsAbs(gitCommonDir) {
+		gitCommonDir = filepath.Join(path, gitCommonDir)
 	}
 
 	// Check for custom hooks path (core.hooksPath)
-	hooksDir := filepath.Join(gitDir, "hooks")
+	hooksDir := filepath.Join(gitCommonDir, "hooks")
 	hooksPathCmd := exec.Command("git", "config", "--get", "core.hooksPath")
 	hooksPathCmd.Dir = path
 	if hooksPathOutput, err := hooksPathCmd.Output(); err == nil {

cmd/bd/doctor/git.go

@@ -30,7 +30,7 @@ var bdHooksRunPattern = regexp.MustCompile(`\bbd\s+hooks\s+run\b`)
 // CheckGitHooks verifies that recommended git hooks are installed.
 func CheckGitHooks() DoctorCheck {
 	// Check if we're in a git repository using worktree-aware detection
-	gitDir, err := git.GetGitDir()
+	hooksDir, err := git.GetGitHooksDir()
 	if err != nil {
 		return DoctorCheck{
 			Name:    "Git Hooks",
@@ -45,8 +45,6 @@ func CheckGitHooks() DoctorCheck {
 		"post-merge": "Imports updated JSONL after git pull/merge",
 		"pre-push":   "Exports database to JSONL before push",
 	}
-
-	hooksDir := filepath.Join(gitDir, "hooks")
 	var missingHooks []string
 	var installedHooks []string
 
@@ -60,13 +58,7 @@ func CheckGitHooks() DoctorCheck {
 	}
 
 	// Get repo root for external manager detection
-	repoRoot := filepath.Dir(gitDir)
-	if filepath.Base(gitDir) != ".git" {
-		// Worktree case - gitDir might be .git file content
-		if cwd, err := os.Getwd(); err == nil {
-			repoRoot = cwd
-		}
-	}
+	repoRoot := git.GetRepoRoot()
 
 	// Check for external hook managers (lefthook, husky, etc.)
 	externalManagers := fix.DetectExternalHookManagers(repoRoot)
@@ -364,8 +356,8 @@ func CheckSyncBranchHookCompatibility(path string) DoctorCheck {
 	}
 
 	// sync-branch is configured - check pre-push hook version
-	// Get actual git directory (handles worktrees where .git is a file)
-	cmd := exec.Command("git", "rev-parse", "--git-dir")
+	// Get common git directory for hooks (shared across worktrees)
+	cmd := exec.Command("git", "rev-parse", "--git-common-dir")
 	cmd.Dir = path
 	output, err := cmd.Output()
 	if err != nil {
@@ -375,14 +367,13 @@ func CheckSyncBranchHookCompatibility(path string) DoctorCheck {
 			Message: "N/A (not a git repository)",
 		}
 	}
-	gitDir := strings.TrimSpace(string(output))
-	if !filepath.IsAbs(gitDir) {
-		gitDir = filepath.Join(path, gitDir)
+	gitCommonDir := strings.TrimSpace(string(output))
+	if !filepath.IsAbs(gitCommonDir) {
+		gitCommonDir = filepath.Join(path, gitCommonDir)
 	}
 
-	// Use standard .git/hooks location for consistency with CheckGitHooks (issue #799)
-	// Note: core.hooksPath is intentionally NOT checked here to match CheckGitHooks behavior.
-	hookPath := filepath.Join(gitDir, "hooks", "pre-push")
+	// Hooks are shared across worktrees and live in the common git directory
+	hookPath := filepath.Join(gitCommonDir, "hooks", "pre-push")
 
 	hookContent, err := os.ReadFile(hookPath) // #nosec G304 - path is controlled
 	if err != nil {

cmd/bd/doctor/quick.go

@@ -24,12 +24,11 @@ func CheckSyncBranchQuick() string {
 // Checks all beads hooks: pre-commit, post-merge, pre-push, post-checkout.
 // cliVersion is the current CLI version to compare against.
 func CheckHooksQuick(cliVersion string) string {
-	// Get actual git directory (handles worktrees where .git is a file)
-	gitDir, err := git.GetGitDir()
+	// Get hooks directory from common git dir (hooks are shared across worktrees)
+	hooksDir, err := git.GetGitHooksDir()
 	if err != nil {
 		return "" // Not a git repo, skip
 	}
-	hooksDir := filepath.Join(gitDir, "hooks")
 
 	// Check if hooks dir exists
 	if _, err := os.Stat(hooksDir); os.IsNotExist(err) {
@@ -94,19 +93,19 @@ func CheckSyncBranchHookQuick(path string) string {
 		return "" // sync-branch not configured, nothing to check
 	}
 
-	// Get git directory
-	cmd := exec.Command("git", "rev-parse", "--git-dir")
+	// Get common git directory for hooks (shared across worktrees)
+	cmd := exec.Command("git", "rev-parse", "--git-common-dir")
 	cmd.Dir = path
 	output, err := cmd.Output()
 	if err != nil {
 		return "" // Not a git repo, skip
 	}
-	gitDir := strings.TrimSpace(string(output))
-	if !filepath.IsAbs(gitDir) {
-		gitDir = filepath.Join(path, gitDir)
+	gitCommonDir := strings.TrimSpace(string(output))
+	if !filepath.IsAbs(gitCommonDir) {
+		gitCommonDir = filepath.Join(path, gitCommonDir)
 	}
 
-	// Find pre-push hook (check shared hooks first)
+	// Find pre-push hook (check shared hooks first via core.hooksPath)
 	var hookPath string
 	hooksPathCmd := exec.Command("git", "config", "--get", "core.hooksPath")
 	hooksPathCmd.Dir = path
@@ -117,7 +116,8 @@ func CheckSyncBranchHookQuick(path string) string {
 		}
 		hookPath = filepath.Join(sharedHooksDir, "pre-push")
 	} else {
-		hookPath = filepath.Join(gitDir, "hooks", "pre-push")
+		// Hooks are in the common git directory, not the worktree-specific one
+		hookPath = filepath.Join(gitCommonDir, "hooks", "pre-push")
 	}
 
 	content, err := os.ReadFile(hookPath) // #nosec G304 - path is controlled

cmd/bd/hooks.go

@@ -51,8 +51,8 @@ func CheckGitHooks() []HookStatus {
 	hooks := []string{"pre-commit", "post-merge", "pre-push", "post-checkout", "prepare-commit-msg"}
 	statuses := make([]HookStatus, 0, len(hooks))
 
-	// Get actual git directory (handles worktrees)
-	gitDir, err := git.GetGitDir()
+	// Get hooks directory from common git dir (hooks are shared across worktrees)
+	hooksDir, err := git.GetGitHooksDir()
 	if err != nil {
 		// Not a git repo - return all hooks as not installed
 		for _, hookName := range hooks {
@@ -67,7 +67,7 @@ func CheckGitHooks() []HookStatus {
 		}
 
 		// Check if hook exists
-		hookPath := filepath.Join(gitDir, "hooks", hookName)
+		hookPath := filepath.Join(hooksDir, hookName)
 		versionInfo, err := getHookVersion(hookPath)
 		if err != nil {
 			// Hook doesn't exist or couldn't be read
@@ -319,19 +319,17 @@ var hooksListCmd = &cobra.Command{
 }
 
 func installHooks(embeddedHooks map[string]string, force bool, shared bool, chain bool) error {
-	// Get actual git directory (handles worktrees where .git is a file)
-	gitDir, err := git.GetGitDir()
-	if err != nil {
-		return err
-	}
-
 	var hooksDir string
 	if shared {
 		// Use versioned directory for shared hooks
 		hooksDir = ".beads-hooks"
 	} else {
-		// Use standard .git/hooks directory
-		hooksDir = filepath.Join(gitDir, "hooks")
+		// Use common git directory for hooks (shared across worktrees)
+		var err error
+		hooksDir, err = git.GetGitHooksDir()
+		if err != nil {
+			return err
+		}
 	}
 
 	// Create hooks directory if it doesn't exist
@@ -401,12 +399,11 @@ func configureSharedHooksPath() error {
 }
 
 func uninstallHooks() error {
-	// Get actual git directory (handles worktrees)
-	gitDir, err := git.GetGitDir()
+	// Get hooks directory from common git dir (hooks are shared across worktrees)
+	hooksDir, err := git.GetGitHooksDir()
 	if err != nil {
 		return err
 	}
-	hooksDir := filepath.Join(gitDir, "hooks")
 	hookNames := []string{"pre-commit", "post-merge", "pre-push", "post-checkout", "prepare-commit-msg"}
 
 	for _, hookName := range hookNames {
@@ -442,13 +439,13 @@ func uninstallHooks() error {
 // runChainedHook runs a .old hook if it exists. Returns the exit code.
 // If the hook doesn't exist, returns 0 (success).
 func runChainedHook(hookName string, args []string) int {
-	// Get the hooks directory
-	gitDir, err := git.GetGitDir()
+	// Get the hooks directory from common dir (hooks are shared across worktrees)
+	hooksDir, err := git.GetGitHooksDir()
 	if err != nil {
 		return 0 // Not a git repo, nothing to chain
 	}
 
-	oldHookPath := filepath.Join(gitDir, "hooks", hookName+".old")
+	oldHookPath := filepath.Join(hooksDir, hookName+".old")
 
 	// Check if the .old hook exists and is executable
 	info, err := os.Stat(oldHookPath)

cmd/bd/init_git_hooks.go

@@ -21,12 +21,12 @@ var preCommitFrameworkPattern = regexp.MustCompile(`(?i)(pre-commit\s+run|prek\s
 
 // hooksInstalled checks if bd git hooks are installed
 func hooksInstalled() bool {
-	gitDir, err := git.GetGitDir()
+	hooksDir, err := git.GetGitHooksDir()
 	if err != nil {
 		return false
 	}
-	preCommit := filepath.Join(gitDir, "hooks", "pre-commit")
-	postMerge := filepath.Join(gitDir, "hooks", "post-merge")
+	preCommit := filepath.Join(hooksDir, "pre-commit")
+	postMerge := filepath.Join(hooksDir, "post-merge")
 
 	// Check if both hooks exist
 	_, err1 := os.Stat(preCommit)
@@ -81,11 +81,10 @@ type hookInfo struct {
 
 // detectExistingHooks scans for existing git hooks
 func detectExistingHooks() []hookInfo {
-	gitDir, err := git.GetGitDir()
+	hooksDir, err := git.GetGitHooksDir()
 	if err != nil {
 		return nil
 	}
-	hooksDir := filepath.Join(gitDir, "hooks")
 	hooks := []hookInfo{
 		{name: "pre-commit", path: filepath.Join(hooksDir, "pre-commit")},
 		{name: "post-merge", path: filepath.Join(hooksDir, "post-merge")},
@@ -137,11 +136,10 @@ func promptHookAction(existingHooks []hookInfo) string {
 
 // installGitHooks installs git hooks inline (no external dependencies)
 func installGitHooks() error {
-	gitDir, err := git.GetGitDir()
+	hooksDir, err := git.GetGitHooksDir()
 	if err != nil {
 		return err
 	}
-	hooksDir := filepath.Join(gitDir, "hooks")
 
 	// Ensure hooks directory exists
 	if err := os.MkdirAll(hooksDir, 0750); err != nil {

cmd/bd/reset.go

@@ -44,8 +44,8 @@ func runReset(cmd *cobra.Command, args []string) {
 
 	force, _ := cmd.Flags().GetBool("force")
 
-	// Check if we're in a git repo
-	gitDir, err := git.GetGitDir()
+	// Get common git directory (for hooks and beads-worktrees, which are shared across worktrees)
+	gitCommonDir, err := git.GetGitCommonDir()
 	if err != nil {
 		if jsonOutput {
 			outputJSON(map[string]interface{}{
@@ -73,7 +73,7 @@ func runReset(cmd *cobra.Command, args []string) {
 	}
 
 	// Collect what would be deleted
-	items := collectResetItems(gitDir, beadsDir)
+	items := collectResetItems(gitCommonDir, beadsDir)
 
 	if !force {
 		// Dry-run mode: show what would be deleted
@@ -82,7 +82,7 @@ func runReset(cmd *cobra.Command, args []string) {
 	}
 
 	// Actually perform the reset
-	performReset(items, gitDir, beadsDir)
+	performReset(items, gitCommonDir, beadsDir)
 }
 
 type resetItem struct {
@@ -91,7 +91,7 @@ type resetItem struct {
 	Description string `json:"description"`
 }
 
-func collectResetItems(gitDir, beadsDir string) []resetItem {
+func collectResetItems(gitCommonDir, beadsDir string) []resetItem {
 	var items []resetItem
 
 	// Check for running daemon
@@ -106,9 +106,9 @@ func collectResetItems(gitDir, beadsDir string) []resetItem {
 		}
 	}
 
-	// Check for git hooks
+	// Check for git hooks (hooks are in common git dir, shared across worktrees)
 	hookNames := []string{"pre-commit", "post-merge", "pre-push", "post-checkout"}
-	hooksDir := filepath.Join(gitDir, "hooks")
+	hooksDir := filepath.Join(gitCommonDir, "hooks")
 	for _, hookName := range hookNames {
 		hookPath := filepath.Join(hooksDir, hookName)
 		if _, err := os.Stat(hookPath); err == nil {
@@ -141,8 +141,8 @@ func collectResetItems(gitDir, beadsDir string) []resetItem {
 		})
 	}
 
-	// Check for sync branch worktrees
-	worktreesDir := filepath.Join(gitDir, "beads-worktrees")
+	// Check for sync branch worktrees (in common git dir, shared across worktrees)
+	worktreesDir := filepath.Join(gitCommonDir, "beads-worktrees")
 	if info, err := os.Stat(worktreesDir); err == nil && info.IsDir() {
 		items = append(items, resetItem{
 			Type:        "worktrees",