Normally changes from git-apply are not worth logging because they
come from a file and can be recovered from there. This option will
mostly be used by add--interactive.pl where patches are generated
during an interactive add session and are very much worth logging.

The logging is a bit more complicated because an update is done in two
phases. The old version of all patches is removed first then the new
one added. We need to keep track of the old version in order to make a
backup.