Ensure all refs are restored on a backup/restore

To restore all refs from a bundle, we need to use the --mirror option to ensure that all refs are properly restored. Without this, refs such as refs/merge-requests/X and refs/keep-around/Y would be omitted, which exposed a bug as described in https://gitlab.com/gitlab-org/gitlab-ce/issues/38319#note_41648608.

Closes #38352 (closed)