refactor protobuf usage throughout

[randypitcherii]

Proto objects in scala may currently use a fragile instantiation. make sure each protobuf useage in the scala applications declare an empty proto object and only uses the getters and setters to fill the proto object.

This will avoid hard to debug errors if proto definitions change over time. A change that would result in a bad proto will be more likely to fail at compile time if we use the getters / setters.