I don't know if it was an oversight or left out for a reason but I found that there was no home page link on the main menu (in the header). I wanted it there and still wanted to maintain {menu_elements} so I added this.
In lib-common.php around line 800 you should see
// Now add nested template for menu items
Just add the following to the top of what is under that line.
// Homepage link
$header->set_var( 'menuitem_url', $_CONF['site_url'] . '/index.php' );
$header->set_var( 'menuitem_text', $LANG01[68] );
$header->parse( 'menu_elements', 'menuitem', true );