Commit 11c5888

@@ -72,7 +72,34 @@ func initRunE(cmd *cobra.Command, args []string, setupWorktree bool) error {
 		return fmt.Errorf("failed to get worktree: %w", err)
 	}
 
-	// Clear the working directory for orphan branch
+	// Clear the index and working directory for orphan branch
+	// This is essential to create a true orphan branch with no parent commits
+	fmt.Println("Clearing working directory for orphan branch...")
+
+	// Get the status to find all tracked files
+	status, err := worktree.Status()
+	if err != nil {
+		return fmt.Errorf("failed to get worktree status: %w", err)
+	}
+
+	// Remove all files from both the index and working directory
+	for filepath := range status {
+		_, err := worktree.Remove(filepath)
+		if err != nil {
+			// Continue even if some files fail to be removed
+			fmt.Printf("Warning: could not remove %s: %v\n", filepath, err)
+		}
+		// Also physically delete the file from disk
+		os.Remove(filepath)
+	}
+
+	// Use RemoveGlob as a fallback to ensure everything is cleared
+	err = worktree.RemoveGlob("*")
+	if err != nil && err != git.ErrGlobNoMatches {
+		fmt.Printf("Warning: RemoveGlob failed: %v\n", err)
+	}
+
+	// Now we have a clean slate for the orphan branch
 	fs := osfs.New(".")
 
 	// Create README.md