Fix extreme near-linear classification

[galjos]

Summary

• tighten near-linear geometry classification
• add QM9 boundary regressions
• validate mode counts across all 133,885 QM9 records

Closes #136

Validation

• 530 passed, 7 skipped; 96% coverage
• QM9: 133,885 geometries and 1,000 thermochemistry calculations passed
• documentation builds with warnings treated as errors

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 95.81%. Comparing base (ae13c2c) to head (28875fb).

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #137   +/-   ##
=======================================
  Coverage   95.81%   95.81%           
=======================================
  Files          34       34           
  Lines        2866     2866           
=======================================
  Hits         2746     2746           
  Misses        120      120           

Flag	Coverage Δ
unittests	95.81% <100.00%> (ø)

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