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EOGenerator templates do not need to be included in your built application so it's best to keep them out of the Resources directory or any other place that is automatically included in the built application. It shouldn't hurt to include them, but there is simply no need to.
"Auto Generate on Build"
You can tell WOLips to automatically trigger the EOGenerator to run the generation process every time the incremental builder is kicked off by turning on "Automatically Run EOGenerator" in the Eclipse Preferences.