Hello, the nightly files sometimes doesn't work properly due to different issues. Sometimes it's a complicated bug but usually it can be fixed easily.
So I put the commands of nightly creator in github  and change cron of pywikibot service to clone this repo and follow it i.e. the nightly creator is automatically loads commands from this repo.
Please report bugs in phabricator (and assign it to me) and pull requests are welcome. pywikibot people like John, Kunal, Merlijn, and Maarten also can push changes and merge pull requests too. If you want to be an owner and I forgot to add you, please do tell me.