How can I remove the hardcoded menus from the Navin subtheme?
&lt;?php
  $main_links = menu_tree_page_data(variable_get('menu_main_links_source', 'main-menu'));
  $main_links = menu_tree_output($main_links);
  $secondary_links = menu_tree_page_data(variable_get('menu_secondary_links_source', 'user-menu'));
  $secondary_links = menu_tree_output($secondary_links);
?&gt;


Get rid of that bit for starters.

If you're not using that, then you can probably also strip out the following:

&lt;?php if ($main_links): ?&gt;
    &lt;nav class="navigation"&gt;
      &lt;?php print render($main_links); ?&gt;
    &lt;/nav&gt;
    &lt;?php endif; ?&gt;
    &lt;?php if ($secondary_links): ?&gt;
    &lt;nav class="navigation-secondary"&gt;
      &lt;?php print render($secondary_links); ?&gt;
    &lt;/nav&gt;
    &lt;?php endif; ?&gt;


Which (for reference) should just leave you with the following:

&lt;div&lt;?php print $attributes; ?&gt;&gt;
  &lt;div&lt;?php print $content_attributes; ?&gt;&gt;
    &lt;?php print $content; ?&gt;
  &lt;/div&gt;
&lt;/div&gt;