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Click on the New Project -> Enterprise, in Choose Project screen, should the Packaged Archive node be listed last, so the different app module node can be listed together without breackage. This can give more logic view to user I feel. Also regarding the node name, I seem to remember one suggested to call it some thing like Deployable Archive or some name can be related to the deployment.
it may have been fixed in 6.0... i don't know.