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The app-controller interface has to provide a data model for describing v4-v6 transtition technologies. The controller-switch interface is pure OF (including the IP-in-IP extensions).
The controller has full knowledge of how to provide any of the v4-v6 transition technology, and is taking care of pre-loading switches with them. If for whatever reason, like a change in network policies (configuration is extremely important if you can make it dynamic and seamless) or a device connected that was impossible to tunnel using a certain deployed technology, the controller would ask the App about what to do with a certain v6 or v4 address, or a certain region of the network, and the App would say something like "apply technology X with parameters X, Y and Z".