What drives the main menu? Hi I'm trying to understand the main menu but it appears to be self populating with the product categories category plus a built in search API (All Products). The main menu also appears disabled in the blocks area?
Can someone explain the mechanics behind this menu please?

Well it looked like from Category>Product category>Edit vocabulary there is an option for Taxonomy menu with a selection list showing Main Menu. I added a new Category to this same structure and now both my new category and the main menu have disappeared from the menu?
I have tried "Select to rebuild the menu on submit." and also removed my new category from main menu... but still the original is missing.
You can see region--menu.tpl.php which is rendering main menu..

&lt;div&lt;?php print $attributes; ?&gt;&gt;   &lt;div&lt;?php print $content_attributes; ?&gt;&gt;
    &lt;?php if ($main_menu || $secondary_menu): ?&gt;
    &lt;nav class="navigation"&gt;
      &lt;div class="primary-menu inline"&gt;
        &lt;?php print theme('links__system_main_menu', array('prefix' =&gt; '&lt;div&gt;', 'links' =&gt; $main_menu, 'attributes' =&gt; array('id' =&gt; 'main-menu', 'class' =&gt; array('links', 'inline', 'clearfix', 'main-menu')), 'heading' =&gt; array('text' =&gt; t('Main menu'),'level' =&gt; 'h2','class' =&gt; array('element-invisible')))); ?&gt;
      &lt;/div&gt;
      &lt;div class="second-menu inline"&gt;
        &lt;?php print theme('links__system_secondary_menu', array('links' =&gt; $secondary_menu, 'attributes' =&gt; array('id' =&gt; 'secondary-menu', 'class' =&gt; array('links', 'inline', 'clearfix', 'secondary-menu')), 'heading' =&gt; array('text' =&gt; t('Secondary menu'),'level' =&gt; 'h2','class' =&gt; array('element-invisible')))); ?&gt;
      &lt;/div&gt;
    &lt;/nav&gt;
    &lt;?php endif; ?&gt;
    &lt;?php print $content; ?&gt;   &lt;/div&gt; &lt;/div&gt;