Run recent version of clang-format on source files

[oskooi]

Manually running clang-format on the source C++ files after updating the pre-commit package to use latest version. Also includes some formatting tweaks and minor updates to the pre-commit yaml file.

Separately, if we ever do decide to limit the line length to 80 characters for all source files, we just need to add an additional argument to the black and clang-format pre-commit hooks (e.g., args: [--line-length=80]).