Flatpak apps mysteriously failing to launch

Finally figured out the mystery of intermittent apps failing to launch on my Fedora/KDE system.

Every so often after a reboot, my browser and other apps, like Slack, seemed to stop launching. Usually rebooting seemed to fix the problem, so I never dug into it.

The problem turned out to be /keybase — a FUSE (filesystem in userspace) mount left behind by Keybase. When the Keybase service crashes or exits uncleanly, the FUSE mount stays behind. Any process that tries to ls / — would hang indefinitely waiting on that dead mount.

Unmounting with sudo umount -l /keybase immediately fixed the issue. I don’t use the keybase app very much so the simplest thing for me to do was to disable the app from running at startup.

What made this so confusing is that Keybase had nothing to do with what I was actually trying to do. It wasn’t installed via Flatpak, I wasn’t using it, and the errors I was seeing (Flatpak bwrap errors, failed pidfiles) pointed nowhere near it. I thought it was related to browser-based apps, like Slack, but that was just a correlation – the apps I typically launch right at startup. The hang was also intermittent — most reboots cleared the stale mount automatically, masking the real cause for months.