Generalize vacuum_storage to handle other file backends

The cleanup of orphan files from storage and the report of missing files that are referenced by the database but not present in storage now go through the file backend, so they will be able to handle other backends once they're implemented.

Empty directories are still only cleaned up from local storage (but that's unlikely to be particularly important for cloud storage), and there's no concept of a non-local upload directory.

Part of #684 (closed).