@takeshitakenji @nbd First of all: queued items (anything related to federation) need to be processed on-load unless you're using background daemons. But making sure the queue is empty by accessing /main/runqueue regularly will do this too.
(one could probably do a sneaky javascript-cron-call-thing, but that's evil)

There's also a comment in the generated config.php about schemacheck. Have a look at that.