Closing a linked doc should correctly remove it from linked docs

* Closing a linked-doc now removes it from root :sub-docs.
  This wasn't happening because a linked doc was calling close-root-document and
  destroying itself before it got to close-linked-document. Since it was
  destroyed there was no way to find its root and update its :sub-docs.
* Closing a linked-doc also unlinks docs with CM.
* Remove destroying root since closing a linked document should not destroy
  a root document which leaves it in an invalid state.