Protobuf now required -- need to make this flexible

[twongjirad]

I hacked the Scons config to build chroma interface and protobuf message. Need to have checks to see if protobuf exists, and, if not, then do not compile Chroma stuff.

[twongjirad]

If the user wants to use Chroma interface, she just needs to specify environment variables. the RAT.scons script should respond accordingly. Need to update documentation.