ATOL does not subscribe to changes at the resource level (see [here](https://github.com/ATL-Research/incremental-class2relational/blob/ccc2a5be33a1e5d9c0a4797ace614fcdd14b4973/solutions/atol/transformation/src/main/java/atol/example/transformation/Run.xtend#L37)) thus it cannot detect added or removed elements at the root. Simple fix would be to add an adapter on the resource and catch add / remove at the root.