fix(sync): support external BEADS_DIR in separate git repository

When BEADS_DIR environment variable points to a separate git repository,
bd sync previously failed with "fatal: 'main' is already used by worktree"
because it computed repoRoot from cwd instead of the beads directory.

This fix detects when beads dir is in a different git repo than cwd and
uses direct git operations (add/commit/push/pull) instead of worktree-based
sync, bypassing the problematic worktree creation entirely.

Cherry-picked from PR #533 (cleaned up unrelated changes).

Co-Authored-By: dand-oss <dand-oss@users.noreply.github.com>

cmd/bd/sync.go

@@ -304,6 +304,73 @@ Use --merge to merge the sync branch back to main branch.`,
 			}
 		}
 
+		// Check if BEADS_DIR points to an external repository (dand-oss fix)
+		// If so, use direct git operations instead of worktree-based sync
+		beadsDir := filepath.Dir(jsonlPath)
+		isExternal := isExternalBeadsDir(ctx, beadsDir)
+
+		if isExternal {
+			// External BEADS_DIR: commit/pull directly to the beads repo
+			fmt.Println("→ External BEADS_DIR detected, using direct commit...")
+
+			// Check for changes in the external beads repo
+			externalRepoRoot, err := getRepoRootFromPath(ctx, beadsDir)
+			if err != nil {
+				fmt.Fprintf(os.Stderr, "Error: %v\n", err)
+				os.Exit(1)
+			}
+
+			// Check if there are changes to commit
+			relBeadsDir, _ := filepath.Rel(externalRepoRoot, beadsDir)
+			statusCmd := exec.CommandContext(ctx, "git", "-C", externalRepoRoot, "status", "--porcelain", relBeadsDir)
+			statusOutput, _ := statusCmd.Output()
+			externalHasChanges := len(strings.TrimSpace(string(statusOutput))) > 0
+
+			if externalHasChanges {
+				if dryRun {
+					fmt.Printf("→ [DRY RUN] Would commit changes to external beads repo at %s\n", externalRepoRoot)
+				} else {
+					committed, err := commitToExternalBeadsRepo(ctx, beadsDir, message, !noPush)
+					if err != nil {
+						fmt.Fprintf(os.Stderr, "Error: %v\n", err)
+						os.Exit(1)
+					}
+					if committed {
+						if !noPush {
+							fmt.Println("✓ Committed and pushed to external beads repo")
+						} else {
+							fmt.Println("✓ Committed to external beads repo")
+						}
+					}
+				}
+			} else {
+				fmt.Println("→ No changes to commit in external beads repo")
+			}
+
+			if !noPull {
+				if dryRun {
+					fmt.Printf("→ [DRY RUN] Would pull from external beads repo at %s\n", externalRepoRoot)
+				} else {
+					fmt.Println("→ Pulling from external beads repo...")
+					if err := pullFromExternalBeadsRepo(ctx, beadsDir); err != nil {
+						fmt.Fprintf(os.Stderr, "Error pulling: %v\n", err)
+						os.Exit(1)
+					}
+					fmt.Println("✓ Pulled from external beads repo")
+
+					// Re-import after pull to update local database
+					fmt.Println("→ Importing JSONL...")
+					if err := importFromJSONL(ctx, jsonlPath, renameOnImport, noGitHistory); err != nil {
+						fmt.Fprintf(os.Stderr, "Error importing: %v\n", err)
+						os.Exit(1)
+					}
+				}
+			}
+
+			fmt.Println("\n✓ Sync complete")
+			return
+		}
+
 		// Check if sync.branch is configured for worktree-based sync (bd-e3w)
 		// This allows committing to a separate branch without changing the user's working directory
 		var syncBranchName string
@@ -1731,3 +1798,106 @@ func resolveNoGitHistoryForFromMain(fromMain, noGitHistory bool) bool {
 	}
 	return noGitHistory
 }
+
+// isExternalBeadsDir checks if the beads directory is in a different git repo than cwd.
+// This is used to detect when BEADS_DIR points to a separate repository.
+// Contributed by dand-oss (https://github.com/steveyegge/beads/pull/533)
+func isExternalBeadsDir(ctx context.Context, beadsDir string) bool {
+	// Get repo root of cwd
+	cwdRepoRoot, err := syncbranch.GetRepoRoot(ctx)
+	if err != nil {
+		return false // Can't determine, assume local
+	}
+
+	// Get repo root of beads dir
+	beadsRepoRoot, err := getRepoRootFromPath(ctx, beadsDir)
+	if err != nil {
+		return false // Can't determine, assume local
+	}
+
+	return cwdRepoRoot != beadsRepoRoot
+}
+
+// getRepoRootFromPath returns the git repository root for a given path.
+// Unlike syncbranch.GetRepoRoot which uses cwd, this allows getting the repo root
+// for any path.
+// Contributed by dand-oss (https://github.com/steveyegge/beads/pull/533)
+func getRepoRootFromPath(ctx context.Context, path string) (string, error) {
+	cmd := exec.CommandContext(ctx, "git", "-C", path, "rev-parse", "--show-toplevel")
+	output, err := cmd.Output()
+	if err != nil {
+		return "", fmt.Errorf("failed to get git root for %s: %w", path, err)
+	}
+	return strings.TrimSpace(string(output)), nil
+}
+
+// commitToExternalBeadsRepo commits changes directly to an external beads repo.
+// Used when BEADS_DIR points to a different git repository than cwd.
+// This bypasses the worktree-based sync which fails when beads dir is external.
+// Contributed by dand-oss (https://github.com/steveyegge/beads/pull/533)
+func commitToExternalBeadsRepo(ctx context.Context, beadsDir, message string, push bool) (bool, error) {
+	repoRoot, err := getRepoRootFromPath(ctx, beadsDir)
+	if err != nil {
+		return false, fmt.Errorf("failed to get repo root: %w", err)
+	}
+
+	// Stage beads files (use relative path from repo root)
+	relBeadsDir, err := filepath.Rel(repoRoot, beadsDir)
+	if err != nil {
+		relBeadsDir = beadsDir // Fallback to absolute path
+	}
+
+	addCmd := exec.CommandContext(ctx, "git", "-C", repoRoot, "add", relBeadsDir)
+	if output, err := addCmd.CombinedOutput(); err != nil {
+		return false, fmt.Errorf("git add failed: %w\n%s", err, output)
+	}
+
+	// Check if there are staged changes
+	diffCmd := exec.CommandContext(ctx, "git", "-C", repoRoot, "diff", "--cached", "--quiet")
+	if diffCmd.Run() == nil {
+		return false, nil // No changes to commit
+	}
+
+	// Commit
+	if message == "" {
+		message = fmt.Sprintf("bd sync: %s", time.Now().Format("2006-01-02 15:04:05"))
+	}
+	commitCmd := exec.CommandContext(ctx, "git", "-C", repoRoot, "commit", "-m", message)
+	if output, err := commitCmd.CombinedOutput(); err != nil {
+		return false, fmt.Errorf("git commit failed: %w\n%s", err, output)
+	}
+
+	// Push if requested
+	if push {
+		pushCmd := exec.CommandContext(ctx, "git", "-C", repoRoot, "push")
+		if output, err := pushCmd.CombinedOutput(); err != nil {
+			return true, fmt.Errorf("git push failed: %w\n%s", err, output)
+		}
+	}
+
+	return true, nil
+}
+
+// pullFromExternalBeadsRepo pulls changes in an external beads repo.
+// Used when BEADS_DIR points to a different git repository than cwd.
+// Contributed by dand-oss (https://github.com/steveyegge/beads/pull/533)
+func pullFromExternalBeadsRepo(ctx context.Context, beadsDir string) error {
+	repoRoot, err := getRepoRootFromPath(ctx, beadsDir)
+	if err != nil {
+		return fmt.Errorf("failed to get repo root: %w", err)
+	}
+
+	// Check if remote exists
+	remoteCmd := exec.CommandContext(ctx, "git", "-C", repoRoot, "remote")
+	remoteOutput, err := remoteCmd.Output()
+	if err != nil || len(strings.TrimSpace(string(remoteOutput))) == 0 {
+		return nil // No remote, skip pull
+	}
+
+	pullCmd := exec.CommandContext(ctx, "git", "-C", repoRoot, "pull")
+	if output, err := pullCmd.CombinedOutput(); err != nil {
+		return fmt.Errorf("git pull failed: %w\n%s", err, output)
+	}
+
+	return nil
+}