Open Build Jars in 6.x. Let's say you have a your primary module, call MainPackage, and the Packaging Method = Copy module output to.
The secondary Jar is SecondaryModule, and Packaging Method = Link via manifest and copy files to.
However, if you open up this project in 7.01b, the main include module MainModule is there, but the SecondaryModule is not. The SecondaryModule shows up in the Project Settings/Global Libraries, but does not show up in the Jar build.