I think the migration from core to plugin is done now for DMs.
This is required since we support the Twitter-based API by default,
which is implemented in many of the mobile clients etc. But you can
disable the DirectMessage for your instance of you wish, of course.
'Bookmark' => array(),
'ClientSideShorten' => array(),
'Directory' => array(),
+ 'DirectMessage' => array(),
'EmailAuthentication' => array(),
'Event' => array(),
'Oembed' => array(),