Updates from properly paying attention to filters in dependent modules
    
    Regenerate flatpak-runtime.yaml with a new version of flatpak-module-tools
    that pays attention to filter: in the mmd. This means we:
    
     Add gtk3
       This is filtered in shared-runtime
     Add graphite2, harfbuzz, libXxf86vm, mesa (for mesa-libEGL)
       These used to be filtered in shared-runtime. This has been fixed
       in dist-git, but not in the current build.
     Add python-setuptools and python-six
       python2-setuptools and python2-six are filtered in base-runtime,
       but we need as indirect dependencies of gobject-introspection..