backends/protobuf/protobuf.cc depends on the source and header files
generated by protoc, but this dependency wasn't explicitly declared. Add
a rule to the Makefile to fix intermittent build failures when the
protobuf header/source file isn't built before protobuf.cc.
o Not all derived methods were marked 'override', but it is a great
feature of C++11 that we should make use of.
o While at it: touched header files got a -*- c++ -*- for emacs to
provide support for that language.
o use YS_OVERRIDE for all override keywords (though we should probably
use the plain keyword going forward now that C++11 is established)