Finish making clang-tidy (mostly) work (again) and run -fix (#2312)

This does some more work to the run_clang_tidy.py wrapper script, and runs an example pass.

"again" because it's really the proto fuzzer changes that broke it, it had been working before.

"mostly" because there's still an issue within the proto fuzzer that it can't find "port/protobuf.h", i.e. https://github.com/google/libprotobuf-mutator/tree/master/port, but I'm still hesitant to add an include path there.

common/string_helpers_test.cpp

@@ -11,7 +11,6 @@
 
 #include "llvm/Support/Error.h"
 
-using ::llvm::toString;
 using ::testing::Eq;
 using ::testing::Optional;