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The layer of j2eeserver module contains stuff which should belong to some project nature, but it is placed directly under the root of the SystemFileSystem. Please, move this in some project nature. These are following folder/files: ProjectEnvironmentsProvider/** Templates/ProfileTypes/**
As described in http://www.netbeans.org/servlets/ReadMsg?msgId=619519&listName=nbdiscuss the current work on projects prototype has been stopped.