I agree. This is probably the biggest impediment to using PMD Eclipse integration on a large project. Checkstyle has the ability to only run against open files. Findbugs has the ability to only run after a file is saved. (not quite as nice). I haven't looked at how checkstyle or findbugs implemented this but they could be used as examples.
Our application has 6000 java files and PMD...
Jacob 1.15 M2 is now available for Download. This is the first release manged through the new SourceForge file management system so post any problems to the discussion groups.