I have a small patch that offers an integration of PMD (http://pmd.sourceforge.net/) into the current build system of JBoss Transaction. Obviously, this is not an highly important feature request, having PMD checking java code is just nice to have. Anyway, as your project is not likely to integrate this patch quickly, I also published the result of a PMD run on the current source code:
(this way you can already check what PMD find out without setting up the tool itself)
I integrated PMD into the qa/ directory which seems the most appropriate directory at first glance... An other strategy would have been to define a "pmd" task inside some common build file ( maybe common/build.xml but it does not look like it), and then have each module call for this anttask with the appropriate java source folder... If you fell this approach is better, please let me know, i'll adapt my patch.
All "violation" detected by PMD are not relevant, a pmd report is just a set of hints of something that may be a bad idea or could be improved.
PMD rulesets (what kind of violation is looking for) are defined in the qa/pmd.xml. In this file you can easily include/exclude rules, and you can use it to configure the PMD Eclipse Plugin.