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Working with Enterprise Application projects can be confusing as all of the project's modules (sub-projects) are at the same level in the tree. This is especially true when other open projects alphabetically insert themselves in between the Enterprise Application projects. Ideally, the module projects belonging to the Enterprise Application project would be listed as sub-projects underneath the EAR project. I've uploaded 2 images that demonstrate the problem: netbeans_projectpane_current.png and netbeans_projectpane_mock.gif. You see in the netbeans_projectpane_current.png that dukesbank-client, which is not a part of the EAR project, falls right in the middle of the EAR project's modules. Compare this with the netbeans_projectpane_mock.gif, which shows a much more friendly project interface.
Created attachment 51736 [details] NetBeans Project Pane with Enterprise Projects - Current View
Created attachment 51737 [details] NetBeans Project Pane with Enterprise Projects - Proposed View
This old bug may not be relevant anymore. If you can still reproduce it in 8.2 development builds please reopen this issue. Thanks for your cooperation, NetBeans IDE 8.2 Release Boss