Provide a callback to customize the repository on clone

Similarly to #2440, provide a callback to customize the repository upon creation for clone. This makes `git_clone_into()` and `git_clone_local_into()` redundant, and they do not implement some of the `git_clone()` logic, so remove them from the API.
Why is this test being removed? I'm sure you have a good reason, it just wasn't immediately obvious to me on the first read through.