[spelech]

Summary

Fixes an unrecoverable repository clone state on Windows when an incremental git fetch fails in a persistent clone directory (keep_shallow=True) and falls back to a fresh git clone:

1. Read-Only .git/objects/pack/* Cleanup on Windows (cleanup_repo_dir):
   • Previously, cleanup_repo_dir called shutil.rmtree(repo_dir, ignore_errors=True). On Windows, Git marks packfiles (.pack / .idx) inside .git\objects\pack as read-only, causing shutil.rmtree to fail with PermissionError and silently leave the non-empty directory behind due to ignore_errors=True.
   • The subsequent git clone then failed permanently with fatal: destination path '...' already exists and is not an empty directory.
   • cleanup_repo_dir now uses an onerror=_handle_remove_readonly callback that clears read-only file attributes (os.chmod(path, stat.S_IWRITE | stat.S_IREAD)) and retries deletion, plus an atomic rename fallback (os.replace) if a handle is briefly held.
2. Incremental Fetch & Fallback Clone Recovery (shallow_clone_repo):
   • Updates the origin remote URL (git remote set-url origin) before running git fetch so token/credential updates take effect on existing clones.
   • Checks git reset --hard return code (falling back to FETCH_HEAD or a fresh clone if reset fails).
   • Ensures repo_dir is cleaned up before the fallback git clone and if the initial --branch clone fails.