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In atomic, containers are left running when docker is restarted. When docker is restarted after the flannel config is put in place, the docker0 interface isn't re-IPed because docker sees the running containers and won't update the previous config. This patch kills all the running containers after docker is stopped. We can't simply `docker stop` the running containers, as they respawn before we've got a chance to stop the docker daemon, so we need to use runc to do this after dockerd is stopped.