Good catch, thank you. You're right that hardening check_optional_file alone just moves the crash: an empty repo returns None there, the loop doesn't skip it, and it then hits repo.get_contents("/") / .github/workflows / .devcontainer in dependabot_file.py, which only catch UnknownObjectException.

I've pushed a follow-up that skips empty repos up front instead:

• Added an is_empty_repo(repo) helper (repo.size == 0, no extra API call since size is already on the listed repo object).
• The main loop now skips empty repos right after the archived check, before any get_contents lookup, so none of the dependabot_file.py paths are reached for them.
• Kept the check_optional_file GithubException 404 handling as a defensive backstop.
• Added unit tests for is_empty_repo; full suite passes (184 passed).

This felt cleaner than broadening the exception handling at each get_contents call site, but happy to switch to a shared safe_get_contents-style helper if you'd prefer that centralization.

I think the shared helper you floated at the end here is worth taking, and I dug up a reason to prefer it over the size == 0 skip. size is GitHub's cached disk-usage number (recalculated asynchronously, roughly hourly), so it isn't a reliable stand-in for "no commits." I confirmed against live repos: jsplumb/jsplumb is public, not archived, has a commit and a README.md, and still reports size: 0. The current skip would log it as "empty repository" and pass it over, so Dependabot never gets enabled there, and freshly pushed repos hit the same window until the cache refreshes.

A small helper that swallows a 404 from either UnknownObjectException or the base GithubException covers the truly-empty case at every call site without the false positive, so we could drop the size == 0 gate entirely:

def list_contents_or_empty(repo, path):
    """Return directory contents at path, or [] when the path is missing or the
    repo is empty. A missing path 404s as UnknownObjectException; an empty repo
    404s as the base GithubException. Both mean "nothing here"."""
    try:
        return repo.get_contents(path)
    except GithubException as e:
        if e.status == 404:
            return []
        raise

Then the three dependabot_file.py loops become for file in list_contents_or_empty(repo, "/"): (and the same for .github/workflows and .devcontainer), their try/except UnknownObjectException blocks go away, and GithubException gets added to the import on line 10. Happy to keep an early skip as well if we base it on a more reliable signal.