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Create a metamodel layer on top of the physical metamodel, which will operate with the project context and will contain associations, rather than symbolic references between individual elements. The metamodel should contain provisions to capture and/or track unresolved referencies, too. The metamodel should contain only a minimal data, rather it should proxy to and associate elements from the Physical metamodel.
There won't be special logical metamodel. It will be part of the Project metamodel. See diagram http://java.netbeans.org/models/java/img/Project.png. You can see three derived associations pointing to the Physical metamodel - HasResources, BelongsTo and Packages. They contain sum of all links for all codebases in classpath. For JavaClass, you can use methods in Classpath element. You can find JavaInterface implementors, JavaClass interfaces, superclasses etc. Similiar methods should be implemented in JavaClass element. (We will use Project instance as a paramater.) See diagram for details.
Done in branch meta_2