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
Update Entity.php
Merge pull request #107 from wmde/setid

Improve Entity::setId