Refactor ProjectTreeRestorer

What does this MR do?

This rewrites a majority of the logic for tree restorer to make it much cleaner in terms of relations between objects and make it much easier to persist objects at very explicit points.

It slightly improves where we store test JSONs, but does not change the outlook of tests, just makes them slightly more strict.

This is based on: !18005 (merged) and !18003 (merged) !18007 (merged)

Does this MR meet the acceptance criteria?

Conformity

• Code review guidelines
• Merge request performance guidelines
• Style guides