Rework handling of missing and duplicated IDs

- UniqueIdUtils:
    - Remove fixMissingIDs(final ITopLevelElement modelElement)
      (only used in one place)
    - fixMissingIDs(EObject object, EObject existingModel): Do not wrap
      model modification into a command. This is up to the caller of
      this method (e.g., the command stack is not available in tests) 
- Remove IDMigrationProvider: Fixup of missing / duplicated is handled
  in ModelContext
- ModelContext: Use nonDirtyingCommand, and automatically save model
  in case IDs have been fixed

Issue-Ref: 3369
Signed-off-by: Simon Barner <barner@fortiss.org>