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/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 {