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.