functions.php

<?php

/**
 * Clean Nav Menu Classes
 *
 */
function ea_clean_nav_menu_classes( $classes ) {

	if( ! is_array( $classes ) )
		return $classes;

	$allowed_classes = array(
		'home',
		'menu-item',
		'current-menu-item',
		'current-menu-ancestor',
		'menu-item-has-children',
	);

	return array_intersect( $classes, $allowed_classes );
}
add_filter( 'nav_menu_css_class', 'ea_clean_nav_menu_classes', 5 );