Changeset for embedded documents calculates to an unnecessary pullAll() and pushAll() in some cases.

When embedded documents are persisted and then some of them are removed in just the right way, the resulting update will issue a $pullAll for ALL of the embedded documents and then a $pushAll on whichever embedded documents weren't actually removed. Obviously, only a $pullAll on the removed items is necessary.

Additionally, while the $pullAll and the $pushAll seem like they should add up to the correct finish (though inefficient), the removed items appear to not be removed correctly. The $pullAll falls correctly into the if loop found here: http://github.com/doctrine/mongodb-odm/blob/master/lib/Doctrine/ODM/MongoDB/Persisters/BasicDocumentPersister.php#L230, but the end result of that $pullAll in this case is that some items are not removed.

A test case for this is here: http://github.com/weaverryan/mongodb-odm/commit/9968697a2c07e31ecfdd8d55ecbf9bf39183d01e. The first case, testModifyGroupsArrayDirectly() tests for this. The second case relates to MODM-79.

Thanks - I've found the issue particular strange to nail down and inconsistent. If you spot any issues in my test cases, let me know.