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.
I used MagicMock because i thought it was 'cooler'.  Turns out it just auto-mocks magic methods, which i don't need.