Alpha quality, use at your own risk.
Modify fluentd-daemonset.yaml as necessary, then run the following:
kubectl create -f fluentd-daemonset.yaml
fluent.conf has Fluentd reading from /var/lib/docker/containers and looking up the container metadata from containers/<id>/config.v2.json.
fluentd-daemonset.yaml has the fluentd-k8s instances reading ES config from environment variables, set up via Kubernetes secrets. Make sure the secrets are set up before provisioning.