Keeping iids number for stable branch

Renumbering iids breaks GitLab references in GFM.
Fixes #5179

### Summary

1. Keep issues, merge requests and milestones number when updating GitLab 6.1.
1. Issues, merge requests and milestones number increments per projects after updating GitLab 6.1.
1. Issues, merge requests and milestones number begin from one at new project.