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When I create a web project with shared libraries and shared server jar files, the IDE adds also javaee6-doc-api.zip to the shared GlassFish_v3 library directory. However, this file is not strictly needed during the headless build - it is only used to show Javadoc when the project is opened in the IDE. It would be useful *not* to copy this file to the shared server library to save space (6MB), and instead bind the IDE copy of this file with the server library, when the user opens the project in the IDE.
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