Admin: Added some links to theme to replace admin menu module

It's not perfect but good enough for me :)

The run-cron is pretty straight forward,
The clear cache I'm still not sure of,
I turned the available updates page into the Drupal Projects link since it's close to doing what the Admin Menu module did in linking to project issue queue.

I think if you could add a "Reports" menu up top next to "People" that would be helpful.

<ul class="links" style="border-top: 3px solid #F5F5F5;">
<li class="path-admin"><a href="<?php check_url($base_path); ?>/admin/reports/status/run-cron">Run Cron</a></li>
<li class="path-admin"><a href="<?php check_url($base_path); ?>admin/settings/performance">Clear Cache</a></li>
<li class="path-admin"><a href="<?php check_url($base_path); ?>admin/reports/updates">Drupal Projects</a></li>
<li class="path-admin"><a href="<?php check_url($base_path); ?>/update.php">Run Updates</a></li>
      </ul>