Federico Cargnelutti has posted an interesting overview that graphically shows outlines for a few major PHP projects showing where the includes are coming from.
The includes of the system map out the dependencies of the system, which files depend on which, which subsystem depends on which. When working with a system, it's always useful to map out the dependencies before hand.
The software he's created the images for include WordPress, phpBB, and a few frameworks - Symfony, Zend Framework and CakePHP. He used the Inclued and Graphviz software to make the charts.
