Restore fixes

Created by: amacarthur

This is dependent upon the following pull request in gitlab-shell: https://github.com/gitlabhq/gitlab-shell/pull/60.

This addresses problems that arise when the backups and repositories directories are in non-default locations. I also have added the option to stifle the need for user confirmation of the rebuild of the authorized_keys file. this is useful if running the restore from a script.

EDIT: This pull request has incorrect commits! Don't pull I will fix