Class loaders work in a tree, and there typically isn't sharing between sibling branches. I believe that visibility is up the tree, and never across. So, you can end up with two different versions of a library existing quite happily in the same process space. Collapsing them down into a single [ejsw?]ar file results in the tree being collapsed down too.

All of a sudden all of the log4j.xml files that everyone has sprinkled everywhere end up overwriting each other...