Add class to primary links menu

1) Agreed. I also like the naked style and 9 out of 10 times i even rip out all that html from those templates. Second i need that class to be on the ul (twitter bootstrap).
2) Guess it will be this option.
3) This option does not give me the option to put the class on the ul right?

Ok, I'll go for option 3.

Would you do it trough a custom pane with php or just programmatically? Don't know if there is any influence on caching or speed? Guess using php in a custom pane will have to go trough eval() every time so that will be slower right?

Second, i don't know if this is a bug but when i tried option two, it went 'wrong' when using the preprocess:

<?php
function indepressie_process_pane_navigation(&$vars) {
  $vars['main_menu'] = theme('links__system_main_menu', array(
    'links' => $vars['main_menu'],
    'attributes' => array('id' => 'main-menu', 'class' => array('nav')),
  ));
}
?>

The template i cleaned up to only $main_menu, but when using the above preprocess it does not return the links, the <ul> is shown but without the inner links.

So im trying to get this done, here is my main_menu.inc

<?php
/**
* This plugin array is more or less self documenting
*/
$plugin = array(
  // the title in the admin
  'title' => t('Main menu'),
  'single' => TRUE,
  'category' => array(t('Everywhere'), -9),
  'render callback' => 'main_menu_pane_content_type_render'
);

function main_menu_pane_content_type_render($subtype, $conf, $args, $context = NULL) {
  $block = new stdClass();
  $block->content = theme('links__system_main_menu', array('links' => $main_menu, 'attributes' => array('id' => 'main-menu-ul', 'class' => array('nav'))));;
  return $block;
}
?>

So now.... :-P, do i have to go as deep as you have with the pane_navigation, as in creating a whole template for this, or can i stick just to code somehow.

//edit: for those creating ctools content types, here's a good tutorial with the basics http://www.nicklewis.org/drupal/tutorials/ctools-custom-content-types

So this is what i would expect:

<?php
function main_menu_pane_content_type_render($subtype, &$context ) {
  $menu = menu_load('main_menu');
	$block = new stdClass();
  $block->content = theme('menu_link', array('links' => $menu, 'attributes' => array('id' => 'main-menu-ul', 'class' => array('nav'))));
  return $block;
}
?>

But that doesn't seem to be it.

Here's what im doing now:

<?php
function main_menu_pane_content_type_render($subtype, &$context ) {
	$menu = drupal_render(menu_tree_output(menu_tree_all_data($pid)));
	$block = new stdClass();
  $block->content = $menu;
  return $block;
}
?>

This prints what i need. Now i only need the get the class in there.

Here's the final working code:
main_menu.inc

<?php
/**
* This plugin array is more or less self documenting
*/
$plugin = array(
  // the title in the admin
  'title' => t('Main menu'),
  'single' => TRUE,
  'category' => array(t('Everywhere'), -9),
  'render callback' => 'main_menu_pane_content_type_render'
);

function main_menu_pane_content_type_render($subtype, &$context ) {
	$pid = variable_get('menu_main_links_source', 'main-menu');
	$menu = drupal_render(menu_tree($pid));
	$block = new stdClass();
  $block->content = $menu;
  return $block;
}
?>

template.php

<?php
function indepressie_menu_tree(&$variables) {
  return '<ul class="menu nav">' . $variables['tree'] . '</ul>';
}
?>