What's changed now is that the ordering is explicitly defined in the .menu file rather than being picked up from the .desktop files. Have a look at the default hildon.menu (it should be in the same directory with an added extension as dpkg couldn't install it) for the details, but there's basically an extra <Layout> section.

Incidentally, all of this can now be done from within the user directory (see /home/user/.config/menus/hildon.menu) so there's no need to modify the system files.