GlassFish Server v2 contained two subdirectories for the applications repository: applications/j2ee-apps and applications/j2ee-modules. Those subdirectories no longer exist in GlassFish Server 3.0.1 (there is no j2ee-apps or j2ee-modules level). Deployment of a standalone module such as foo.war, which was previously located in applications/j2ee-modules/foo in GlassFish Server v2, is now located in applications/foo in GlassFish Server 3.0.1. Enterprise applications and standalone modules essentially share the same name space, so the intermediate directory layer was not necessary.