fixes for gitlab restore with non-standard backup and repo dirs

NOTE These are dependent upon the following pull request on gitlab-shell: https://github.com/gitlabhq/gitlab-shell/pull/60

These fixes will allow a restore of gitlab when the backups and repositories directories are in non-standard locations (ie sub-dirs of gitlabhq). Also allows the restore to be run from script overriding the need of a user to confirm the rebuild of the authorized_keys file.