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.
What were the changes you made to these tests around changing None to Secret.get()? It seems unrelated to your change, and I think the tests pass either way?