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
It seems we are talking about different thinks. The old implementation may be deprecated, but it's gone. This is an abstract interface now. It's obviously not deprecate. Both implementations use it.