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When you install a plugin to deploy to a particular server (Weblogic, Websphere, Geronimo, Tomcat, etc), a Server Runtime Environment is added (See Eclipse Preferences > Server > Runtime Environments). If you have a standard Java Project (no EJB, Web or Server connections) and add this runtime to your Build path, it is equivalent to adding a User Library. The Import Eclipse Project tool in NetBeans does not include this runtime's jars.
Not planning on working on noncritical Eclipse importer bugs for 6.8.
David would better understand what needs to be done.
Sounds like yet another XML file should be taken from Eclipse workplace and imported similarly as other user defined libraries. Should be easy but low priority.
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