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.

explorer/fuzzing/ast_to_proto.cpp

@@ -772,7 +772,7 @@ static auto DeclarationToProto(const Declaration& declaration)
   return declaration_proto;
 }
 
-Fuzzing::CompilationUnit AstToProto(const AST& ast) {
+auto AstToProto(const AST& ast) -> Fuzzing::CompilationUnit {
   Fuzzing::CompilationUnit compilation_unit;
   *compilation_unit.mutable_package_statement() =
       LibraryNameToProto(ast.package);