http://www.ii.uni.wroc.pl/~nthx/blog/blog_19012005.html might help a little bit.
Take care - Tomasz Nazar
PS. It may be little out dated. If so, notify me please..
PS2. There is of course entry in official JBAOP docs about your problem: "packaging aspects" or sth similar..
The trouble stems from using expanded war archives, actually. But thanks for the pointer.