I have run into another annoying problem building exploded ears -
I had some jars attached to my web module, decided they may be bad so I removed them all and attached new versions.
There is no longer a reference anywhere in the settings to the old jars, as far as I can tell.
However, when I build the ear that references the web module, both versions of the jars show up in the WEB-INF/lib of the exploded directory.
In the ear (non-exploded) version, the jars are not duplicated under WEB-INF/lib.
Note: Closing the project and re-opening does not seem to fix the problem.