phpDocumentor is the standard auto-documentation tool for PHP. 
Written in PHP, phpDocumentor can be used directly from the 
command-line, or through an easy to use web interface.  It can
be used to generate professional documentation directly from the 
source code of your PHP project.  Support for linking between 
documentation, automatic class inheritance and generation of 
highlighted source code with cross-referencing to php general 
documentation are just a few of the features of phpDocumentor. 

You can override DOCROOT, PHPUSER, and PHPGROUP at build time.
They default to DOCROOT=/var/www/htdocs, PHPUSER=root, PHPGROUP=apache.