flatpak: update manifest
Several updates to the flatpak manifest:
- Update poppler to version 0.79.0 and libgxps to 0.3.1.
- Remove openjpeg and enchant2 since they're already included in the runtime.
- Remove unused build features and files from evince, poppler, and libgxps.
- Use a https url for popplerdata instead of http.
- Add gnome-desktop module. This is needed to cache thumbnails on the Recent Documents screen.