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.
+1 to removing. I don't think we should lose too much sleep over "perfect" backwards compatibility until we actually start getting issues and feedback from external users.