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I got the following scenario: I got a base class that's annotated with @MappedSuperclass and has an @Id. If I know extend the class everything is fine, netbeans reports everything to be valid. Now I extend the baseclass with another class and again extend this class and netbeans reports a missing @Id. Compiled with Maven the class works as expected as it gets the id from the first class. I guess netbeans is not going through the full class hierarchy to determine if there is an @Id annotation.
Can you provide example project. I can reproduce error mark, but also if I deploy application with entity->some class->mapped superclass I have runtime error, and I do not have one if it's just entity->mapped superclass. And also all is fine in netbeans and at runtime if both parents are annotated with MappedSuperClass.