Filter out built-in wp_nav_menu classes but keep custom class

One of the darker corners of the code. 🙂 Here is my take:

add_filter('nav_menu_css_class', 'discard_menu_classes', 10, 2);

function discard_menu_classes($classes, $item) {

    return (array)get_post_meta( $item->ID, '_menu_item_classes', true );
}