Display 'Main menu' with sub links

In the base template stark, I tried: <?php print_r($main_menu); ?>, and $main_menu doesn't carry any of the sub link items I created... Maybe a remaining bug?
I'm relatively new to Drupal so I'm not really sure if we should create an Issue for that...? I might miss something. Just in case: http://drupal.org/node/add/project-issue/drupal.

I have been searching for hours now and found no solution to this yet. If anyone knows how to achieve this please link to the solution.

I wish I could delete my post - I realise now that it's probably not very relevant to v7. Might be useful to someone using v6.

This is a simplified version of how I themed my menus (in Drupal 6.15):

page.tpl.php:

...
<?= $navbar ?>
...

menu_tree.tpl.php:

<ul><?= $tree ?></ul>

menu_item.tpl.php:

<li><?= $link.$menu ?></li>

menu_item_link.tpl.php:

<a href="/<?= $item['href'] ?>"><?= $item['title'] ?></a>

A more advanced version of menu_tree.tpl.php - my submenu markup was different to the top-level menu so I changed includes/menu.inc and includes/common.inc (not recommended) to pass in the level of the menu and the parent link:

menu_tree.tpl.php:

<? 
switch ($level){
	case 0:?>
		<ul class="nav-primary"><?= $tree ?></ul><? 
		break;
			
	case 1:
		$class='nav-submenu';
		if ($parentLink['in_active_trail'])
    		    $class .= ' active-trail';?>
                <ul class="<?=$class ?>"><?=$tree?></ul><?
                break;
?>

changes to menu.inc:

0737:function menu_tree_output($tree, $level=0, $parentLink=null) {
0760:$output .= theme('menu_item', $link, $data['link']['has_children'], menu_tree_output($data['below'], $level+1, $data['link']), $data['link']['in_active_trail'], $extra_class, $data['link']);
0766:return $output ? theme('menu_tree', $output, $level, $parentLink) : '';
1139:function theme_menu_tree($tree, $level, $link) {

changes to common.inc:

3099:'arguments' => array('tree' => NULL, 'level' => 0, 'parentLink' => NULL),

Same here...

The other way to solve it:

Create a region for menu (if there are no suitable yet) and then just enable main links block there. This will hopefully will be the only way for D8, but I use this technique starting from D5. Works like charm.

UPD: of course you'll have to style that menu block.

I found this thread when I came upon the same issue in Drupal 6. (I'm assuming "main menu" in D7 is the equivalent of "primary links" in D6.) Here's my solution in case anyone can make use of it:

1) Define a custom theme hook (template.php)

function my_theme_theme(&$existing, $type, $theme, $path) {
	...
	
	// custom theme function for single ubiquitous site menu
	// (using Drupal default primary links menu, BUT with full tree output, not single level.)
	$hooks['full_site_menu'] = array(
		'arguments' => array(
			// if NULL, function checks variable 'menu_primary_links_source'
			'menu_name' => NULL
		)
	);
	
	...
	return $hooks;
}

2) Implement the output function (template.php)

// our theme's custom primary links menu theme function
// note when a theme (rather than a module) registers a hook,
// the assumed function name will be [theme_name]_[hook_name] ... not theme_[hook_name]
function my_theme_full_site_menu($menu_name = NULL) {

	if(is_null($menu_name)) {
		$menu_name = variable_get('menu_primary_links_source', 'primary-links');
	}

	// outputs the full hierarchy of this menu
	return menu_tree($menu_name);
}

3) Use it (probably in page.tpl.php)

    <nav id="site-menu">
        <?php print theme('full_site_menu'); // custom, registered by our theme ?>
    </nav>

-

... and it's ridiculous that it isn't, here's the simple steps. This turns your menu into a menu tree with as many levels as you want (can be all of them). After this, you can add whatever CSS or JS you want to this to make them open or close or expand or dropdown or whatever on mouseover, click, etc.

• Get the Menu Block module (stable for D5, D6, D7, probably will be for D8...)
• Go to the Blocks page ( Structure > Blocks in D7 ) and click Add New Menu Block
• Click Advanced Settings (it looks like it does nothing, but it adds a few options further down the page). Tick Expand all, and set it to start at level 1, continue to level 'Unlimited'

This prints to the page the whole output for the whole menu tree structured like this (may have more/less classes depending on theme). It doesn't impose anything else, it just gives you the whole Drupal menu in the HTML output to do your own thing with:

<div class="menu-block-wrapper">
  <ul class="menu">
     <li class="first leaf">
         <a href="/some-link">Some link</a>
     </li>
     <li class="expanded">
         <a href="/some-link">Some link</a>
         <ul class="menu">
             <li class="first leaf">
                <a href="/some-link">Some link</a>
             </li>
             <li class="last leaf">
               <a href="/some-link">Some link</a>
             </li>
         </ul>
     </li>
     <li class="last leaf">
         <a href="/some-link">Some link</a>
     </li>
  </ul>
</div>

Please try this instead,

<?php
  $main_menu_tree = menu_tree(variable_get('menu_main_links_source', 'main-menu')); 
  print drupal_render($main_menu_tree);
?>

Hope this helps.

To render all menus from main menu define the following function in your theme's template.php file

function THEMENAME_preprocess_page(&$variables) {
// Get the entire main menu tree
$main_menu_tree = menu_tree_all_data('main-menu');

// Add the rendered output to the $main_menu_expanded variable
$variables['main_menu_expanded'] = menu_tree_output($main_menu_tree);
}

Then, in page.tpl.php, you can just use:

print render($main_menu_expanded);