To get what I wanted I started using some !PhpDocumenter with customized smarty templates. Later I added some PHP and regular expressions to post-process the output of !PhpDocumenter. I ran into a few things and ended up having to modify !PhpDocumenter to output more information, or in a different way. The order in which I approached the problem directly reflects how much a pain it is to accomplish.
Unfortunately I personally have found the !PhpDocumenter code-base is huge, is written for PHP 4 and, ironically, is not documented that well. I know there is an effort with http://www.docblox-project.org/ to make a modern PHP docblock parser. Unfortunately it only runs on PHP 5.2, so I won't be able to use it for the foreseeable future since this server is stuck on 5.1.6 due to CentOS/Plesk.
I wish the Flourish doc generation was something simpler. I also wish the site was a simple configuration of Trac (or even mtrack now that it exists). Some decade when I have a ridiculous amount of free time I will port everything over to newer and better systems.