Flatpak apps cannot prompt for the file manager on Fedora GNOME templates

[solene]

You need to install xdg-desktop-portal-gtk

Joplin, what is the best way to use it on Qubes?

install the package xdg-desktop-portal-gtk (maybe xdg-desktop-portal-gnome or xdg-desktop-portal but the first should be enough), flatpak requires xdg-portal to offer a file picker