Fix docker restart in atomic

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.