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Create a layer.xml file in a NetBeans module (in the New File wizard, choose Module Development | XML Layer). Once you have created the layer.xml file, expand it in the Important Files node, find the item you want to remove, right-click on it, choose Delete. The _hidden tag for the layer folder or file will be added to your layer.xml file.
Alternatively, if you know the applicable names of folders or files, add the information to the layer.xml file yourself, e.g:
<folder name="Menu"> <folder name="File"> <file name="org-netbeans-modules-project-ui-NewFile.shadow_hidden"/> </folder> </folder>