Picking the wrong app when having both system and flatpak ones

[jle64]

It sometimes makes sense to have two versions of an app installed, one using flatpak and the other not. For exemple, on Fedora Silverblue, Firefox is part of the base system and can't really be removed, but you might want to also install the Flatpak version which comes with more codecs by default.

In that case, you end up with two versions of the .desktop file, one in /usr/share/applications/org.mozilla.firefox.desktop and another in /var/lib/flatpak/exports/share/applications/org.mozilla.firefox.desktop. Gnome uses the second one, but Junction picks the first one, preventing using the flatpak version.

I've been able to circumvent this by removing Junction's permission to access the /usr version with Flatseal, which makes him pick the right one, but it would be better if it behaved like Gnome by default.