Application archives (EAR files) and component archives (JAR, WAR, and RAR files) that are deployed in the source server do not require any modification to run on Oracle GlassFish Server 3.0.1. Components that may have incompatibilities are deployed on GlassFish Server 3.0.1 with the compatibility property set to v2 and will run without change on GlassFish Server 3.0.1. You may, however, want to consider modifying the applications to conform to Java EE 6 requirements.
The Java EE 6 platform specification imposes stricter requirements than Java EE 5 did on which JAR files can be visible to various modules within an EAR file. In particular, application clients must not have access to EJB JAR files or other JAR files in the EAR file unless they use a Class-Path header in the manifest file, or unless references use the standard Java SE mechanisms (extensions, for example), or use the Java EE library-directory mechanism. Setting this property to v2 removes these Java EE 6 restrictions.
Applications and components that are deployed in the source server are deployed on the target server during the upgrade. Applications that do not deploy successfully on the target server must be deployed manually on the target server by the user.
If a domain contains information about a deployed application and the installed application components do not agree with the configuration information, the configuration is migrated as is without any attempt to reconfigure the incorrect configurations.