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.
The function doesn't exist anymore, and we're already testing that a plain `git_clone` does append to above. Since it went down to clone_into anyway, this test was probably redundant even when it existed.