So, if I do the following:
$x = new X;
$em->persist($x);
$em->flush(); // this updates $x in the Neo4j, as I would expect...
$x->setFoo('bar');
$em->flush(); // $x should update
But it doesn't work unless I add another $em->persist($x) after the flush. I would expect that flush() would not effect which entities are managed, but it seems that flushing is effectively executing a clear() as a side effect.
Are my expectations out of whack or is this a bug?