Application structure

Dabbled in here with XMind and what you saw above was born. The picture is clickable, leads to XMind.net where you can download the mind map itself representing the directory structure of one of the applications on the Zend Framework. If you look closely, you can see some comments. Why is this? The manual is not very beautifully displayed, plus can someone give any suggestions or share ideas / solutions. You can post ideas either here or on XMind.