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.
Should we switch the location of this parameter in the struct with `remote_cb`? (Same thing for `repository_cb_payload` and `remote_cb_payload`.) It seems like since repository precedes remote in creation, that we would want to have that order in the options struct as well.