kodobanin: 
    cd proto
    rm *.pb.c *.pb.h
    ./tools/nanopb-0.2.8-macosx-x86/generator-bin/protoc --nanopb_out=. morpheus_ble.proto

kitsune:   
    cd proto
    rm *.pb.c *.pb.h
     ./tools/nanopb-0.3.1-macosx-x86/generator-bin/protoc --nanopb_out=. sync_response.proto
     ./tools/nanopb-0.3.1-macosx-x86/generator-bin/protoc --nanopb_out=. morpheus_ble.proto
     ./tools/nanopb-0.3.1-macosx-x86/generator-bin/protoc --nanopb_out=. periodic.proto
     ./tools/nanopb-0.3.1-macosx-x86/generator-bin/protoc --nanopb_out=. audio_data.proto
     ./tools/nanopb-0.3.1-macosx-x86/generator-bin/protoc --nanopb_out=. log.proto
     ./tools/nanopb-0.3.1-macosx-x86/generator-bin/protoc --nanopb_out=. matrix.proto
 Java:      
    protoc --java_out=. *.proto


Then move the generated file to the right place, or specify the output path using --nanopb_out param.