Flushing new collections

this includes and fixes https://github.com/doctrine/phpcr-odm/pull/477, https://github.com/doctrine/phpcr-odm/pull/480 and https://github.com/doctrine/phpcr-odm/pull/483

I assume there is still room to simplify a lot of code related to changeset computation since we can now always expect a PeristentCollection. speaking of which we do not yet convert ChildrenCollections.