PMD 4.0.1 was released a few days ago and is not available in the new official site: https://sourceforge.net/projects/pmd/files/pmd-eclipse/update-site/

It appears that this site also fixes the issue we got with Partial IU ( https://sourceforge.net/p/pmd/bugs/1098/ ) and should simply get mirrored (no need for regenerating p2 metadata)