abhigyanpatwari/GitNexus · error · ValueError

repository root must be a real directory: {root}

Error message

repository root must be a real directory: {root}

What it means

All errors below are raised by internal helpers of `eval/workflow_bench/promotion_apply.py` and propagate to the caller of the public entry points: `apply_promoted_overlay(overlay, repo_root, *, expected_digest, expected_target_bases)`, `destination_base_digests(overlay, repo_root)`, `committed_destination_base_digests(overlay, repo_root, *, ref)` and `freeze_overlay(overlay, destination)`. The module applies promoted skill overlays across the canonical skill tree plus its shipped mirrors (`gitnexus/skills`, `gitnexus-claude-plugin/skills`) in a TOCTOU-hardened, symlink-rejecting, descriptor-bound transaction. After `lstat`/`resolve` succeed, `_open_repository_root` checks `stat.S_ISLNK(metadata.st_mode) or not stat.S_ISDIR(metadata.st_mode)`. A symlink-to-a-dir, a regular file, a socket, or any non-directory trips the guard. The repository root must be a literal on-disk directory.

Source

Thrown at eval/workflow_bench/promotion_apply.py:158

    if (
        stat.S_ISLNK(final.st_mode)
        or not stat.S_ISREG(final.st_mode)
        or not (identity(before) == identity(opened) == identity(after) == identity(final))
    ):
        raise ValueError(f"overlay destination changed while being read: {target}")
    return b"".join(chunks), opened.st_mode


def _open_repository_root(repo_root: Path) -> tuple[Path, int]:
    root = repo_root.expanduser().absolute()
    try:
        metadata = root.lstat()
        resolved = root.resolve(strict=True)
    except OSError as exc:
        raise ValueError(f"repository root is unavailable: {root}") from exc
    if stat.S_ISLNK(metadata.st_mode) or not stat.S_ISDIR(metadata.st_mode):
        raise ValueError(f"repository root must be a real directory: {root}")
    if resolved != root:
        raise ValueError(f"repository root must not traverse symlinks: {root}")
    flags = os.O_RDONLY | os.O_DIRECTORY | getattr(os, "O_CLOEXEC", 0) | getattr(os, "O_NOFOLLOW", 0)
    try:
        descriptor = os.open(root, flags)
    except OSError as exc:
        raise ValueError(f"repository root changed while opening: {root}") from exc
    try:
        opened = os.fstat(descriptor)
        final = root.lstat()
        final_resolved = root.resolve(strict=True)

        def identity(value: os.stat_result) -> tuple[int, int, int]:
            return value.st_dev, value.st_ino, stat.S_IFMT(value.st_mode)

        if (
            stat.S_ISLNK(final.st_mode)
            or not stat.S_ISDIR(opened.st_mode)

View on GitHub (pinned to d540b00184)

Solutions

1. Inspect the entry: `pathlib.Path(root).lstat()` and confirm `S_ISDIR` and not `S_ISLNK`.
2. Replace any symlink with a real directory (`readlink` then bind-mount or move).
3. Re-derive and pass the real checkout directory explicitly.

Example fix

// before
root = Path('/repo')  # /repo -> /data/checkout (symlink)
apply_promoted_overlay(overlay, repo_root=root)
// after
root = Path('/data/checkout')  # the real directory
assert root.is_dir() and not root.is_symlink()
apply_promoted_overlay(overlay, repo_root=root)

def assert_real_dir(p):
    root = Path(p).expanduser().absolute()
    st = root.lstat()
    if stat.S_ISLNK(st.st_mode) or not stat.S_ISDIR(st.st_mode):
        raise ValueError(f'repo_root must be a real directory, got: {root}')
    return root

import stat
def is_real_directory(p: str) -> bool:
    root = Path(p)
    try:
        st = root.lstat()
    except OSError:
        return False
    return (not stat.S_ISLNK(st.st_mode)) and stat.S_ISDIR(st.st_mode)

except ValueError as exc:
    if 'must be a real directory' in str(exc):
        raise SystemExit(f'repo_root is a symlink or non-directory: {exc}')

When it happens

Trigger: Pointing `repo_root` at a symlink (even one targeting a real dir), a regular file, or any non-directory filesystem entry.

Common situations: Operator symlinked the checkout for convenience; `repo_root` accidentally resolves to a tarball/sparse-file; default `REPO_ROOT` miscomputed via `parents[N]` after a file move.

Related errors

• repository root must not traverse symlinks: {root}
• overlay destination parent must not be a symlink: {target}
• {label} must be a real directory: {lexical}: {exc}
• {label} must be a real directory: {lexical}
• {label} must not traverse symlinks: {lexical}

AI-assisted analysis of abhigyanpatwari/GitNexus@d540b00184 (2026-08-12). Data as JSON: /api/errors/375c9f6b5b4f9bdc. Report an issue: GitHub.