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It would be nice if all files generated into a project could have a license header included when the template is created, and new files created from template could automatically have the header prepended. Probably ideal would be a flat text license file in nbproject/, and possibly a modification to DataObject.createFromTemplate() to allow header text to be passed in (and the DataObject would then comment it appropriately in a file-type-dependent way).
Fixed in 6.0: just modify project.properties to contian project.license=GPL, etc.