I believe they are talking about the Dokku commands that are needed to set up a new Dokku app.
For example for a static site that would be the following:
dokku apps:create dewey.at
dokku domains:set dewey.at dewey.at www.dewey.at
dokku letsencrypt:enable dewey.at
That's also one of my wishes to get improved, currently I just have a long text file where I store them so that if I move servers I can just re-run them if needed.