Fix things up to make running clang-tidy easier. #2246
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run_clang_tidy.py (the clang-tools-extras version) is parallel so should be feasible to work with. I'm trying to codify this mainly because finding out the right invocation can be difficult.
This fixes some loading of re2 and proto that's started to become an issue.
It's hard to see actual issues because of the identifier length warning being turned off in #2244, and just general issue creep. There may be more fixes to do but this should still be an improvement.