One of the interactions between Medley and Git is the handling of deleting a file from the repo.
If I have on my local disk FOO FOO.~1~ and FOO.~2~ and with some git action that updates FOO (checkout of another branch), it recovers OK : git will break the hard link between FOO and FOO.~2~ and Lisp will see FOO;3.
But things aren't so good if the checkout deletes FOO because FOO.~1~ and FOO.~2~ are still around. Lisp will see INFILEP(FOO) finding FOO:2.
At the very least, a github "hook" could warn the user when the checkout deleted a file while there are ~nn~ versions.
In fact, this doesn't really have to do with git and it could be in lisp. Just detect when file versions are in a state that conflicts with Lisp's expectations: