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I created a new Basic Java Desktop Application, but didn't need the status bar, so I selected it in the Inspector and deleted it. Suddenly my source was full of red. The delete had not removed the associated event listeners! My NetBeans version is: Product Version: NetBeans IDE Dev (Build 20080520075433) Java: 1.6.0_05; Java HotSpot(TM) Client VM 10.0-b19
The GUI builder takes care about code in initComponents() method and about event listeners added using GUI builder's UI e.g. through Events menu item or Events tab in Properties. The code outside these guarded sections is treated as if it was added manually (e.g. handcoded) and as such is not automatically removed e.g. must be removed manually becuase was manually added. It probably was not obvious for Java Desktop Application because the code in question was not added manually by you, but by author of this template. Maybe we should consider possibility to specify (in the corresponding wizard) that some parts of the application (like status bar or menu) should not be generated. Feel free to fill an enhancement about that.