Since Lab Management 2.4, background processes (crons) are run by a job manager. The manager ensures that a job isn't run if another instance is running, kills off long-running or stuck jobs, records statistics about the jobs, and more.
Fundamental job definitions are picked up from installation-support/default-conf/cubit/cubit-runtime.conf whenever recreate-runtime.py is run. Unless there's a specific reason - say you need to add a new cron job for root or Apache, or override an existing job definition - you're encouraged to NOT edit the definition in site.conf.