Various cleanups that are possible with Frames 2.3.1.

 - the doc unit getAgent method has been renamed to getRepository,
   and now returns a single item instead of an iterator.
 - there is no need to explicitly compare vertices to determine if
   a pair of frames are the same, since the equals() method now compares
   vertices for us.
 - updates transaction handling.
Merge branch 'master' into tp-2.4.0-sparql