Teach "stg assimilate" to repair patch reachability

Rewrite "stg assimilate" so that it in addition to assimilating
commits made on top of the patch stack also will rewrite the
applied/unapplied files to reflect reality. A patch is considered to
be applied if it is reachable from HEAD without passing through a
merge, and unreachable otherwise.

Performance is adequate: On my laptop, it takes less than four seconds
to process the Linux tree (with hot caches).

Signed-off-by: Karl Hasselström <kha@treskal.com>