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After you have harvested assets, it is not feasible to modify the system-supplied relationships. It is, however, possible to add relationships manually.
One strategy is to publish the service candidate (or whatever type you are working with), and document it there for development. After the implementation is harvested, the harvested service would need to be attached manually to the original service candidate.
I don't believe that adding annotations to the code will help with your use case, however upon harvesting a WSDL, OER should be picking up the WSDL description in the annotation and populating the service description in OER.