Remove the ability to clone shallow

- We discovered fetching a ref that depends on commits which are not
in the repo (because the repo was cloned 'shallow') causes errors.
- This disables the shallow cloning option entirely, and for backward
compatibility it detects if an existing repo is shallow and re-clones
it if so.
Can we use our `self.patch()` helper instead of the decorator form? I think it's more readable and also consistent with how we've been writing tests up to this point.