Fix orphan removal on clear and embed relations with references

I've added several tests that were failing on orphan removal.

- Using clear() on a persistent collection did not trigger the orphan removal process.

- Removing an embedded document from a collection did not trigger the orphan removal process. This is needed to trigger cascade operations when the embedded document references another document. (A embeds B, B references C, removing B from A did not trigger any cascade remove on C)