In order to resolve some of the merge errors, `theirs` project is added
a parameter to `apply_change_to_project` to compensate for lost
information about components that were removed from `project`.

Some refactorings:
- When checking if something is a PBXGroup using `is_a`, there's no need
  to check if it's a PBXVariantGroup because it inherits from PBXGroup.