I just got really nerd-sniped and rewrote my command-line launcher generator for Flatpak in Python+PyGObject, solving pretty much every flaw it had along the way.

If you've been reluctant to use Flatpak-packaged apps because of the bad command-line user experience, give it a try. Aside from not being able to expose manpages that were just plain omitted from the packages, I'd call it perfect in all ways that matter.

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