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.
Feedback from review

- Remove references to shallow
- Change test patching
Merge pull request #47 from box/delete_repo_if_shallow

Remove the ability to clone shallow