Old question but since there still seems to be interest in it… I just installed the PTI plugin and there was no mention of PHPMD so I wonder where you get the “Mess Detection” menu item from?
For me actually nothing of PTI works with Eclipse Kepler SR2. Whatever I try just nothing happens.
I’d recommend you MakeGood for running PHPUnit tests in Eclipse and setting up Jenkins (including PHPMD) for your project, it takes a bit time to set up but once it is running it is just great: Template for Jenkins Jobs for PHP Projects