Update omnibus to account for multiple mount points

gitlab-org/gitlab-ce!4657 introduces a new application setting to select the default repository storage path for the new multiple git mount point feature (see gitlab-org/gitlab-ce!4578). Omnibus must be updated to account for this new setting.

See https://gitlab.com/gitlab-org/gitlab-ee/issues/583 for more details about the feature.

/cc @maratkalibek @marin