better main menu with bootstrap theme.

template.php

function my_theme_preprocess_page(&$variables) {
  if ($variables['main_menu']) {
    // Build links.
    $links_source = variable_get('menu_main_links_source', 'main-menu');
    $tree = menu_tree_all_data($links_source, NULL, 1);
    menu_tree_add_active_path($tree);

    $variables['primary_nav'] = menu_tree_output($tree);
    // Provide default theme wrapper function.
    $variables['primary_nav']['#theme_wrappers'] = array('menu_tree__primary');
  }
}