Previous elements such as web-module, ejb-module, and so on are deprecated in GlassFish Server 3.0.1 and replaced with the new application element. For more information about the application element, see application in Oracle GlassFish Server 3.0.1 Domain File Format Reference.
During an upgrade, GlassFish Server v2 applications are redeployed at the new applications/ location with the new application element in domain.xml. Any new applications deployed on GlassFish Server 3.0.1 will be deployed with the new directory structure and element.