Comment 3 for bug 818925

Sorry to spam - this seems to be a gnome-menus issue and not a dupe of the above mentioned bug
gnome-menus should install both an applications.menu and a settings.menu to /etc/xdg/menus
Then when alacarte is run they will be created in ~/.config/menus

For gnome-shell I believe it was decided to change from gnome-applications.menu to applications.menu, you just need to include a settings.menu