Move the CMDEPLOY_STAGES=install execution into the Dockerfile these
operations baked into the image layer. On container start, only
configure and activate stages run by default. Users can override with
CMDEPLOY_STAGES="install,configure,activate" to force a full reinstall
without rebuilding the image.
Also fixes CERTS_MONITORING_TIMEOUT typo in docker-compose.yaml (was
"$CERTS MONITORING TIMEOUT"), and replaces the docker-commit workaround
in docs with CMDEPLOY_STAGES documentation.
