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It seems that I have made some mistakes which I can only correct by breaking a few things.
1) I had to move the descriptor.proto and 2) rename the union plugin to onlyone.
1)
The fact that gogoprotobuf extends the descriptor.proto means is has to import it. I have placed it in code.google.com/p/gogoprotobuf/protoc-gen-gogo/descriptor which is not a problem in Go or Java from my experience. It seems that the C++ generated code also imports the generated descriptor code located in google/protobuf/ This causes a conflict, since you can't have two descriptors.
The descriptor.proto is imported as such "google/protobuf/descriptor.proto" gogoprotobuf rewrites this import as "code.google.com/p/gogoprotobuf/protoc-gen-gogo/descriptor" where the generated code, descriptor.pb.go, is located.
Next the union extension causes C++ to generate code which conflicts with the union keyword. I have changed the union keyword to onlyone, since a union can only have one value and their can only be one union. There can only be one ;) This will require users of the union extension to edit their proto files.