How to enable the Flatpak application shortcut in Qubes OS?
The Qubes documentation has detailed steps on how to add a shortcut only for a given AppVM or make it available from the template to all VMs. I decided to add it from the template, so that I can click on the Qubes Setting menu and add it for the exact AppVM. I did not want to modify the required files in dom0 by hand. The reason: just being lazy.
From my AppVM (where I have the Flatpak application installed), I copied the desktop file and also the icon to the template (Fedora 29 in this case).
Then in the template, I moved the files to their correct locations. I also modified the desktop file to mark that this is a Flatpak application.
sudo cp ~/QubesIncoming/xchat/io.github.Hexchat.desktop /usr/share/applications/io.github.Hexchat.desktop
sudo cp ~/QubesIncoming/xchat/io.github.Hexchat.png /usr/share/icons/hicolor/48x48/
After this, I refreshed, and then added the entry from the Qubes Settings, and, then the application is available in the menu.