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.

toolchain/lexer/token_kind_test.cpp

@@ -19,7 +19,7 @@ using ::testing::MatchesRegex;
 // We restrict symbols to punctuation characters that are expected to be widely
 // available on modern keyboards used for programming.
 constexpr llvm::StringLiteral SymbolRegex =
-    "[\\[\\]{}!@#%^&*()/?\\\\|;:.,<>=+~-]+";
+    R"([\[\]{}!@#%^&*()/?\\|;:.,<>=+~-]+)";
 
 // We restrict keywords to be lowercase ASCII letters and underscores.
 constexpr llvm::StringLiteral KeywordRegex = "[a-z_]+";