to_disk: Represent revisions as empty directories instead of symlinks

The symlink representation is slightly ambiguous, so not necessarily very useful. Additionally, it made directory-flat bundles differ from a non-recursive 'git clone' checkout, which confuses Guix and potentially other tools.

We may revisit this in the future, eg. by adding a dotfile in the directory or metadata at the root.

Resolves #4349 (closed)

cc @seirl