I know this bug is marked as a "Feature" and you are merely in bug fixing mode at this point, but I think it'd be critically bad if one of the main new features of the J2EE Module support isn't accessible using the API. I need this in order for the Orion and Resin plugins to be updated to work perfectly with the very common setup of:
source in src/java
JSPs in src/webapp
jars in lib/runtime
Without this, I'm back to the same uselessness I had in 3.0. PLEASE think about adding support for this.