Mapping and Organizing PHP
<p>I have a website that is mainly written in PHP and it seems impossible to remember how everything stitches together.  I'd like to redo the entire website into the Codeigniter or Kohana MVC format, but before I do so; I need to organize how my code is arranged.  Are there any applications or methods available for organizing PHP websites?</p>

<p>EDIT: It should be made clear that I don't want to reorganize the actual code itself, but to find a way to map out the current code I have.  I wish to reorganize the code itself later when I switch to a MVC format.</p>
