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MD-SAL interaction is available at both Java and REST(CONF) level, with Java being the primary one at this point.

The choice of which level to integrate in depends largely on the language of your choice and the interaction pattern you expect to use. If you are an end-user kind of application, which uses ODL to talk to the network, REST should be fine. If you end up providing programmatic interfaces on your northbound, a Java plugin would be better, as you can model your NB using the same means as MD-SAL and automatically have them consistent with the rest of ODL.

I cannot really comment on the terminology question. As for deprecation ... no AD-SAL is not officially deprecated, but it seems that more of the community's projects are centered around MD-SAL concepts and infrastructure.