WordPress’s menu feature is a fantastic way of creating a hierarchical menu, but unfortunately you still have to keep your pages in their own, separate hierarchy, using a horribly cumbersome interface, or a special plugin. The code snippet below will adjust your page hierarchy to match your menu, every time you edit your menu (so long as javascript is turned on). It does this by changing post_parent and menu_order for any pages that are no longer in sync with the menu. Pages that are not in the menu are not changed. To use the function in your own plugin, on the first line, you’ll need to enter the id of the menu you want to keep in sync.

The function gets the details of the menu by calling get_term_by, whilst wp_get_nav_menu_items returns all of the items in the menu. Finally, wp_update_post modifies any pages that need to be changed.

<?php
add_action ('wp_update_nav_menu', 'emw_create_hierarchy_from_menu', 10, 2);

function emw_create_hierarchy_from_menu($menu_id, $menu_data = NULL) {
	if ($menu_id != 1)  // You should update this integer to the id of the menu you want to keep in sync
		return;
	if ($menu_data !== NULL) // If $menu_date !== NULL, this means the action was fired in nav-menu.php, BEFORE the menu items have been updated, and we should ignore it.
		return;
	$menu_details = get_term_by('id', $menu_id, 'nav_menu');
	if ($items = wp_get_nav_menu_items ($menu_details->term_id)) {
	    // Create an index of menu item IDs, so we can find parents easily
		foreach ($items as $key => $item)
    		$item_index[$item->ID] = $key;
    	// Loop through each menu item
		foreach ($items as $item)
			// Only proceed if we're dealing with a page
			if ($item->object == 'page') {
				// Get the details of the page
				$post = get_post($item->object_id, ARRAY_A);
				if ($item->menu_item_parent != 0)
					// This is not top-level menu items, so we need to find the parent page
					if ($items[$item_index[$item->menu_item_parent]]->object != 'page') {
						// The parent isn't a page. Queue an error message.
						global $messages;
						$messages[] = '<div id="message" class="error"><p>' . sprintf( __("The parent of <strong>%1s</strong> is <strong>%2s</strong>, which is not a page, which means that this part of the menu cannot sync with your page hierarchy.", ETTD), $item->title, $items[$item_index[$item->menu_item_parent]]->title) . '</p></div>';
						$new_post['post_parent'] = new WP_Error;
					} else
						// Get the new parent page from the index
						$new_post['post_parent'] = $items[$item_index[$item->menu_item_parent]]->object_id;
				else
					$new_post['post_parent'] = 0; // Top-level menu item, so the new parent page is 0
				if (!is_wp_error ($new_post['post_parent'])) {
					$new_post['ID'] = $post['ID'];
					$new_post['menu_order'] = $item->menu_order;
					if ($new_post['menu_order'] !== $post['menu_order'] || $new_post['post_parent'] !== $post['post_parent'])
						// Only update the page if something has changed
						wp_update_post ($new_post);
				}
			}
	}
}
?>