Improve Entity::setId

* $item->setId( 42 ) is no longer deprecated (integer argument)
* $entity->setId is now deprecated (the whole method)
* $item->setId( $entityId ) is still deprecated though now is type hinted as such

Also brings us one step closer to killing Entity
As far as I understand, the notion of *all* Entities having a setId() method is deprecated, while we want Item and Property to indeed have such a method (but potentially not other kinds of Entity).

It would be good to have that documented clearly. In the current form, it's a bit confusing.