The configure.php changes in phpdoc/ are completely separate from PhD. All PhD needs is a file containing the XML (i.e. .manual.xml) which can be created with PHP:
On a related note, it's worth mentioning that using "configure.php" is a temporary measure until PhD-Setup (its replacement) exists. Gwynne is working on that now but I'm sure she would enjoy some collaboration with others too.
Also, welcome to the team Rudy! :) Regards, Philip