diff --git a/internal/cmd/polecat.go b/internal/cmd/polecat.go
index 54df8d1d..7948ed51 100644
--- a/internal/cmd/polecat.go
+++ b/internal/cmd/polecat.go
@@ -1203,8 +1203,15 @@ func runPolecatNuke(cmd *cobra.Command, args []string) error {
 		}
 
 		// Step 4: Delete branch (if we know it)
+		// Use bare repo if it exists (matches where worktree was created), otherwise mayor/rig
 		if branchToDelete != "" {
-			repoGit := git.NewGit(filepath.Join(p.r.Path, "mayor", "rig"))
+			var repoGit *git.Git
+			bareRepoPath := filepath.Join(p.r.Path, ".repo.git")
+			if info, err := os.Stat(bareRepoPath); err == nil && info.IsDir() {
+				repoGit = git.NewGitWithDir(bareRepoPath, "")
+			} else {
+				repoGit = git.NewGit(filepath.Join(p.r.Path, "mayor", "rig"))
+			}
 			if err := repoGit.DeleteBranch(branchToDelete, true); err != nil {
 				// Non-fatal - branch might already be gone
 				fmt.Printf("  %s branch delete: %v\n", style.Dim.Render("○"), err)
diff --git a/internal/polecat/manager.go b/internal/polecat/manager.go
index 421fad60..e3d0df93 100644
--- a/internal/polecat/manager.go
+++ b/internal/polecat/manager.go
@@ -445,21 +445,17 @@ func (m *Manager) RemoveWithOptions(name string, force, nuclear bool) error {
 		}
 	} else {
 		// GT-1L3MY9: git worktree remove may leave untracked directories behind.
-		// Clean up any leftover .beads/ directory that wasn't fully removed.
-		cloneBeadsDir := filepath.Join(clonePath, ".beads")
-		_ = os.RemoveAll(cloneBeadsDir)
-		// Remove the now-empty clonePath if it still exists
-		_ = os.Remove(clonePath)
+		// Clean up any leftover files (overlay files, .beads/, setup hook outputs, etc.)
+		// Use RemoveAll to handle non-empty directories with untracked files.
+		_ = os.RemoveAll(clonePath)
 	}
 
-	// Also remove the parent polecat directory if it's now empty
+	// Also remove the parent polecat directory
 	// (for new structure: polecats/<name>/ contains only polecats/<name>/<rigname>/)
 	if polecatDir != clonePath {
-		// GT-1L3MY9: Clean up any orphaned .beads/ directory at polecat level.
-		// This can happen if the worktree cleanup was incomplete or from old state.
-		polecatBeadsDir := filepath.Join(polecatDir, ".beads")
-		_ = os.RemoveAll(polecatBeadsDir)
-		_ = os.Remove(polecatDir) // Non-fatal: only removes if empty
+		// GT-1L3MY9: Clean up any orphaned files at polecat level.
+		// Use RemoveAll to handle non-empty directories with leftover files.
+		_ = os.RemoveAll(polecatDir)
 	}
 
 	// Prune any stale worktree entries (non-fatal: cleanup only)