Do your flatpak .desktop files go into a different directory to your regular ones?
this post was submitted on 12 Apr 2026
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It seems to depend on the package. Don't know enough of Flatpak to determine if there is some sort of system-wide setting to manage this.
- Luanti, Stellarium, Norka, PPSSPP: they seem to place an entry in
export/share/applicationswithin each flatpak application dir, plus a copy (not a link) in/usr/share/applications, all formatted with the package name (eg.: "org.gnome.gnucash" or something). The native menu entry is hidden by the flatpak one, despite the native still existing in/usr/share/applications, so eg.: listing the entries in the menu or searching by name always shows one entry, and it's always the Flatpak one. - Apostrophe, Nheko: They place their desktop entry in the flatpak exports dir, then they remove or overwrite the native desktop entry from
/usr/share/applications. Reinstalling the native application makes the file reappear, but not the desktop entry (which I guess gets subsumed into the case above). - Gnucash, Mousepad: they place their entry in the flatpak exports dir, and a copy (not a link) in
/usr/share/applications. However, these entries seem to not conflict, as the menu always shows two entries when searching for the application.