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The node XML Layer is not visible if all Layer entries are generated by annotations, such that no layer.xml is needed. However, if there is added an empty layer.xml to the project all entries generated by annotations are displayed as wanted. It would be nice if the check whether the node should be displayed or not includes a check for layer generating annotations.
Or simply display \build\classes\META-INF\generated-layer.xml below the "Important files" node.