Teach "stg assimilate" to repair patch reachability

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>