Add a 'bottom' parameter to Series.refresh_patch and use it

By specifying a bottom for the new patch commit, it is no longer
necessary to update the bottom of the patch before calling
refresh_patch.  This ensures that the patch top always correspond to a
commit object, and the bottom to its parent.

Signed-off-by: David Kågedal <davidk@lysator.liu.se>
Signed-off-by: Karl Hasselström <kha@treskal.com>