I'm looking to convert PHPDocumentor output to a format I can traverse through in PHP (Ideally, I want an array of all the functions with their comments).
Is there any way to do this?
Zend_Reflection might be of some use: http://framework.zend.com/manual/en/zend.reflection.reference.html
Another option would be to use the parse option of DocBlox to generate a XML structure which you can then interpret with your own code.
After you have installed DocBlox using PEAR you can use the following command to generate a structure.
docblox parse -d [SOURCE_FOLDER] -t [TARGET_LOCATION]
or
docblox parse -f [SOURCE_FILE] -t [TARGET_LOCATION]