do not rename .aToM but only .atom projects in migration

Sorry @DouweM forgot to add this.

See https://gitlab.com/gitlab-org/gitlab-ce/merge_requests/2651/diffs#bc35672f73f4ee025132aee428f383acdf0f755e_0_51

Fixes https://gitlab.com/gitlab-org/gitlab-ce/issues/3699

See merge request !2712