fix(worktree): add -f flag to handle missing but registered state (#609)

Problem:
When the daemon auto-sync runs with --auto-commit --auto-push, the sync
branch pull operation consistently fails with:

  fatal: '.git/beads-worktrees/beads-metadata' is a missing but already
  registered worktree; use 'add -f' to override, or 'prune' or 'remove'
  to clear

This occurs because:
1. Daemon creates worktree at .git/beads-worktrees/<branch>
2. Git registers it in .git/worktrees/<branch>
3. After the operation, worktree contents are removed
4. Git registration persists, pointing to the now-empty path
5. Subsequent CreateBeadsWorktree calls fail because os.Stat() returns
   error (path missing), so no cleanup happens, then git worktree add
   fails because git still has it registered

Root cause:
The git worktree add commands in CreateBeadsWorktree() did not use the
-f (force) flag, which is needed to override the "missing but already
registered" state.

Solution:
Add -f flag to both git worktree add commands (for existing branch and
new branch cases). Per git documentation, -f overrides the safeguard
that prevents creating a worktree when the path is already registered
but missing.

The existing git worktree prune call (line 30-32) was intended to handle
this, but it runs before the path check and may not always clear the
registration in time. The -f flag provides a robust fallback.

Testing:
- All existing worktree tests pass
- Added regression test TestCreateBeadsWorktree_MissingButRegistered
  that simulates the exact issue #609 scenario

Fixes #609

Co-authored-by: Charles P. Cross <cpdata@users.noreply.github.com>

internal/git/worktree.go

@@ -52,13 +52,15 @@ func (wm *WorktreeManager) CreateBeadsWorktree(branch, worktreePath string) erro
 	branchExists := wm.branchExists(branch)
 
 	// Create worktree without checking out files initially
+	// Use -f (force) to handle "missing but already registered" state (issue #609)
+	// This occurs when the worktree directory was deleted but git registration persists
 	var cmd *exec.Cmd
 	if branchExists {
 		// Checkout existing branch
-		cmd = exec.Command("git", "worktree", "add", "--no-checkout", worktreePath, branch)
+		cmd = exec.Command("git", "worktree", "add", "-f", "--no-checkout", worktreePath, branch)
 	} else {
 		// Create new branch
-		cmd = exec.Command("git", "worktree", "add", "--no-checkout", "-b", branch, worktreePath)
+		cmd = exec.Command("git", "worktree", "add", "-f", "--no-checkout", "-b", branch, worktreePath)
 	}
 	cmd.Dir = wm.repoPath
 

internal/git/worktree_test.go

@@ -1056,3 +1056,65 @@ func TestIsWorktree(t *testing.T) {
 		}
 	})
 }
+
+// TestCreateBeadsWorktree_MissingButRegistered tests the issue #609 scenario where
+// the worktree directory is deleted but git still has it registered in .git/worktrees/.
+// The -f flag on git worktree add should handle this gracefully.
+func TestCreateBeadsWorktree_MissingButRegistered(t *testing.T) {
+	repoPath, cleanup := setupTestRepo(t)
+	defer cleanup()
+
+	wm := NewWorktreeManager(repoPath)
+	worktreePath := filepath.Join(t.TempDir(), "beads-worktree-gh609")
+	branch := "beads-metadata-gh609"
+
+	// Step 1: Create a worktree
+	if err := wm.CreateBeadsWorktree(branch, worktreePath); err != nil {
+		t.Fatalf("Initial CreateBeadsWorktree failed: %v", err)
+	}
+
+	// Verify it exists and is registered
+	if _, err := os.Stat(worktreePath); os.IsNotExist(err) {
+		t.Fatal("Worktree was not created")
+	}
+
+	// Step 2: Manually delete the worktree directory (simulating the bug scenario)
+	// but leave the git registration in .git/worktrees/
+	if err := os.RemoveAll(worktreePath); err != nil {
+		t.Fatalf("Failed to remove worktree directory: %v", err)
+	}
+
+	// Verify the directory is gone
+	if _, err := os.Stat(worktreePath); !os.IsNotExist(err) {
+		t.Fatal("Worktree directory should not exist after removal")
+	}
+
+	// Verify git still has it registered (this is the "missing but registered" state)
+	cmd := exec.Command("git", "worktree", "list", "--porcelain")
+	cmd.Dir = repoPath
+	output, err := cmd.CombinedOutput()
+	if err != nil {
+		t.Fatalf("Failed to list worktrees: %v", err)
+	}
+	if !strings.Contains(string(output), "worktree") {
+		t.Log("Note: git worktree list shows no worktrees - prune may have run")
+	}
+
+	// Step 3: Try to recreate the worktree - this should succeed with -f flag (issue #609 fix)
+	// Without the fix, this would fail with:
+	// "fatal: '.git/beads-worktrees/...' is a missing but already registered worktree"
+	if err := wm.CreateBeadsWorktree(branch, worktreePath); err != nil {
+		t.Errorf("CreateBeadsWorktree failed for missing-but-registered worktree (issue #609): %v", err)
+	}
+
+	// Verify the worktree was recreated successfully
+	if _, err := os.Stat(worktreePath); os.IsNotExist(err) {
+		t.Error("Worktree was not recreated after issue #609 fix")
+	}
+
+	// Verify it's a valid worktree
+	valid, err := wm.isValidWorktree(worktreePath)
+	if err != nil || !valid {
+		t.Errorf("Recreated worktree should be valid: valid=%v, err=%v", valid, err)
+	}
+}