Fix Importing labels and milestones associations - Import/Export

Fixes https://gitlab.com/gitlab-org/gitlab-ce/issues/19510 and https://gitlab.com/gitlab-org/gitlab-ce/issues/19447
- [x] [CHANGELOG](https://gitlab.com/gitlab-org/gitlab-ce/blob/master/CHANGELOG) entry added
- Tests
  - [x] Added for this feature/bug
  - [x] All builds are passing
- [x] Conform by the [style guides](https://gitlab.com/gitlab-org/gitlab-ce/blob/master/CONTRIBUTING.md#style-guides)
- [x] Branch has no merge conflicts with `master` (if you do - rebase it please)
- [x] [Squashed related commits together](https://git-scm.com/book/en/Git-Tools-Rewriting-History#Squashing-Commits)

See merge request !5426
Signed-off-by: Rémy Coutable <remy@rymai.me>

Fix MR diff encoding issues exporting projects

Fixes https://gitlab.com/gitlab-org/gitlab-ce/issues/19338

See merge request !5039

added changelog

added better error handling. Also refactored some of the code and fixed a few issues in project_tree_saver