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.
Any reason why you chose this instead of:

os.path.isfile(os.path.join(self._repo_directory, '.git', shallow)) ?