flatpak: Update Flatpak manifests

Update GitHub Flatpak builds to latest runtime version, add new libs
that we need and remove the ones that are not needed anymore.

pkgs/flatpak/com.github.rafostar.Clapper-nightly.json

@@ -31,7 +31,6 @@
         "--filesystem=xdg-run/gvfsd",
         "--own-name=org.mpris.MediaPlayer2.Clapper",
         "--talk-name=org.gtk.vfs.*",
-        "--talk-name=org.gnome.Shell",
         "--env=GST_PLUGIN_SYSTEM_PATH=/app/lib/gstreamer-1.0"
     ],
     "build-options": {