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Eclipse allows for a headless build of the workspace. There should be a command which allows to export WAR or EAR file from a headless build operation. Right now, exporting a WAR or EAR file is only possible from the GUI, which makes it little useful automated builds.
This is supported programatically. Write an application that calls WebComponentExportDataModelProvider. See http://www.eclipse.org/webtools/jst/components/j2ee/api/j2ee_operationsAPI.html for details.