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Bug 381443 gives an example where adding null annotations to a super class is perceived as burdensome, because all sub classes may need to be updated (manually or via quick fix / cleanup). The most elegant solution would be to add null annotations via the Change Method Signature refactoring, and let it propagate null annotations to overriding methods in sub classes.
Yes, the refactoring should support annotations on the method (return type) as well as on parameters. This is also interesting for annotations other than the null annotations.