Ordering $links with theme_links and hook_link_alter

For this to work you need to know the index of the links you want to force the order on. There is a line of code at the start of the function commented out that you can remove the comment from to see the link indexes. This code goes in your themes template.php file. If your theme does not have such a file you will need to create it, in this the file needs to start with <?php.

This may not be best practices since use the links_alter hook might be better but requires an array copy and would need to be implemented in a module. This version on the other hand directly calls theme_links at the end.

function phptemplate_links($links = array(), $delimiter = ' | ') {
  /**
* catches the theme_links function
*/
	// Uncomment the following line to see the links and the indexes
	// print '<pre>' . print_r($links, TRUE) . '</pre>';
	
	$ordered_links = array();
	
	// Indexes of links we want to force order for 
	// Links accounted for here will be in order in this array
	
	$in_order = array('taxonomy_term_1', 'taxonomy_term_2');
	
	// Move links we care about to $ordered_links array
	//   Will be added in order index is found in $in_order array
	
	foreach ( $in_order as $index ) {
		// Make sure the link exists
		if( isset($links[$index]) ) {
			$ordered_links[] = $links[$index];
			unset($links[$index]);
		}
	}
	
	// Add any links not accounted for at end
	
	foreach ( $links as $link ) {
		$ordered_links[] = $link;
	}

	// Not really a best practice but it avoid copying
	//	the code in theme_links
	
	return theme_links($ordered_links, $delimiter);
}