Can't get template.php functions used in Zen subtheme.

EDIT: I may have realised what the problem is, or at least part of it. I've been focussing on Zen's page.tpl.php section

<?php if ($primary_links): ?>
    <div id="primary" class="clear-block">
        <?php print theme('links', $primary_links); ?>
    </div> <!-- /#primary -->
<?php endif; ?>

The problem with this, is that I'm using the standard blocks primary links with Zen's own primary links display turned off. Result? This code isn't being called at all because the links display reverts to control of the Drupal core. You can just about tell this because Zen's div has ID "primary" while Drupal's blocks div has ID "block-menu-primary-links".

This doesn't exlain why eclectus_links isn't being used yet but it certainly explains why nothing custom or even a basic print statement work.

If I solve this completely I'll post it as a comment.

END OF EDIT.

Before anyone refers me to the obvious documentation, here's what I've tried so far (where eclectus is the subtheme name):

• templates.php is copied from the Zen STARTERKIT directory.
• I have copied theme_links from theme.inc and renamed it eclectus_links so it now reads function eclectus_links($links, $attributes = array('class' => 'links')) .
• I know this file is being parsed because I missed out a closing bracket when copying and it immediately broke my site.
• 'Rebuild theme registry on every page' is on.
• I went to Admin -> Site Config -> Performance and hit 'Clear cached data' anyway.
• I went to Site Building -> Themes -> settings -> Eclectus and hit 'Save configuration' (a necessary extra step, I have found)

I got nothing.

Here is what I have read:

• http://drupal.org/node/173880
• http://drupal.org/node/11811 including all the links in the comments.
• http://drupal.org/node/457242 inclulding Tidbit's comment near the bottom.
• http://www.group42.ca/theming_101_the_theme_links_function which seems hideously out of date now.
• http://api.drupal.org/api/function/theme_links/6
• http://adaptivethemes.com/add-span-tags-to-primary-links-for-sliding-doo...

In the foreach loop, I've added a basic

if (!empty($link['title'])) {
	$link['title'] = $i . ': ' . $link['title'];
}
 

for testing so it now reads:

function eclectus_links($links, $attributes = array('class' => 'links')) {
  global $language;
  $output = '';

  if (count($links) > 0) {
    $output = '<ul'. drupal_attributes($attributes) .'>';

    $num_links = count($links);
    $i = 1;

    foreach ($links as $key => $link) {
      $class = $key;

      // Add first, last and active classes to the list of links to help out themers.
      if ($i == 1) {
        $class .= ' first';
      }
      if ($i == $num_links) {
        $class .= ' last';
      }
      if (!empty($link['title'])) {
        $link['title'] = $i . ': ' . $link['title'];
      }
      if (isset($link['href']) && ($link['href'] == $_GET['q'] || ($link['href'] == '<front>' && drupal_is_front_page()))
          && (empty($link['language']) || $link['language']->language == $language->language)) {
        $class .= ' active';
      }
      $output .= '<li'. drupal_attributes(array('class' => $class)) .'>';

      if (isset($link['href'])) {
        // Pass in $link as $options, they share the same keys.
        $output .= l($link['title'], $link['href'], $link);
      }
      else if (!empty($link['title'])) {
        // Some links are actually not links, but we wrap these in <span> for adding title and class attributes
        if (empty($link['html'])) {
          $link['title'] = check_plain($link['title']);
        }
        $span_attributes = '';
        if (isset($link['attributes'])) {
          $span_attributes = drupal_attributes($link['attributes']);
        }
        $output .= '<span'. $span_attributes .'>'. $link['title'] .'</span>';
      }

      $i++;
      $output .= "</li>\n";
    }

    $output .= '</ul>';
  }
}
 

Nothing.

I've also tried dropping in

function eclectus_indylinkclass ($links) {
	$message = '\n<!-- eclectus_indylinkclass: nothing -->\n';
	$eye = 1;

	if (count($links) > 0)
	{
		$message =  '\n<!-- \n';
		foreach ($links as $link)
		{
			$message .= 'eclectus_indyclasslinks' . $eye . ': ' . $link['href'] . "\n";
			++$eye;
		}
		$message .= '-->\n';
	}
	
	return $message;
}

with the intention of trying to alter only the primary links before they hit theme_links (yes, I will be checking that) but no comments appear in my source code when I call it in page.tpl.php as either $eclectus_indyclasslink or indyclasslink. No ouput, no errors.

This is driving me somewhat bananas.