It's breaking the access to the website and not a good look for the "app store for Linux". A lesson in central points of failure?
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https://www.flathub.org is using Let’s encrypt. Their certs only last 90 days so you need a script to make sure they are updated and pushed to your site. https://flathub.org uses Globalsign which lasts for 13 months. My guess is they don’t have a process for reconciling the two types of end dates.
It’s not hard to automate? I remember when Firefox had this same flub, lol
Even just manually, how hard is it to put a reminder in a calendar somewhere? I've never understood how/why this happens, it's really but difficult.
You don't even need to automate. Certbot comes with a systemd timer called
certbot-renew.timerwhich does this for you.