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

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.
Correction to restore expected current directory
Merge pull request #4140 from amacarthur/restore-fixes-clean

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