Safer ref updates

Use `git update-ref` to prevent clobbering concurrent ref updates. If
rugged/libgit2 is temporarily confused, due to concurrent `git gc` for
example, then it used to be possible to accidentally reset a ref to an
earlier state and lose commits. Because `git update-ref` does not get
confused by `git gc`, what will happen now is that the commit based on
confused information fails, preventing data loss.

Fixes https://gitlab.com/gitlab-org/gitlab-ce/issues/20353

See merge request !6130