refactor: update more to clang tools v19

[jnooree]

Checklist

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• Does ./scripts/run_clang_tools.sh pass without any warnings?
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This is a follow-up PR of #379.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 90.57%. Comparing base (456f4d8) to head (db5fc7c).
Report is 6 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #380      +/-   ##
==========================================
- Coverage   90.57%   90.57%   -0.01%     
==========================================
  Files          39       39              
  Lines       10554    10553       -1     
==========================================
- Hits         9559     9558       -1     
  Misses        995      995              

Files with missing lines	Coverage Δ
include/nuri/core/element.h	96.49% <100.00%> (ø)
include/nuri/core/molecule.h	85.24% <100.00%> (ø)
include/nuri/utils.h	97.82% <100.00%> (ø)
src/fmt/sdf.cpp	84.58% <100.00%> (-0.03%)	⬇️