add(129.0.0_python_exec_transition.sh): gracefully upgrade python-exec

We've had trouble with eclean and equery vanishing in our SDKs from time
to time. Although I don't know the root cause it seemed to be some
confusion in the ebuild environment, perhaps a mis-match between the
eclasses, profiles, and ebuilds. Updating all of those seemed to resolve
the issue and to make sure other environments are ok force a re-install
of portage and gentoolkit to clean things up.