Cleanup of planted git files handles links and retries failed paths

Claude Code can remove git files that were planted in a folder to make it behave like a bare repository, a git repository with no working files. This cleanup now sorts paths by how deep they sit in the folder tree and retries the ones whose check failed. Before, it only deleted files, in one pass.

On Windows, it now treats a worktrees entry as a link or junction, a kind of shortcut to another folder, rather than as an ordinary folder. This behaviour is behind a flag.