Error: opendir(refs/remotes): No such file or directory

I have an issue where, every time I update, something will fail because of a “opendir(refs/remotes): No such file or directory” error and I can’t figure out how to fix it.

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Thanks to the help of someone in the Matrix room, I solved the problem by uninstalling all my Flatpak applications, removing the Flathub remote, uninstalling Flatpak itself, deleting the /var/lib/flatpak directory, reinstalling Flatpak, readding the Flathub remote and reinstalling all the applications.