Address quality stewardship issues

[newtontech]

Summary

• add a shared BaseWavefunctionAnalysis interface and adopt it in orbital/fuzzy analyzers
• centralize element symbol lookup and remove repeated parser lookup tables
• simplify parser detection, VASP support declarations, overlap type lookup, and bond-order atom-pair loops
• replace noisy parser/core debug prints with logging and remove unused placeholder modules
• add quality reports plus reference validation coverage for five molecules

Issues

Closes #8
Closes #9
Closes #10
Closes #11
Closes #12
Closes #13
Closes #14
Closes #15
Closes #16
Closes #17
Closes #18
Closes #19

Verification

• uv run --group dev pytest tests/quality/test_quality_refactors.py tests/validation/test_reference_molecule_framework.py --no-cov -> 11 passed
• uv run --group dev pytest tests/analysis/test_bonding.py tests/analysis/test_population.py tests/math/test_density.py --no-cov -> 109 passed, 16 skipped for missing external example files
• uv run --group dev pytest --no-cov -> 482 passed, 43 skipped for missing optional fixtures/integration flags
• git diff --check -> clean
• docs presence check from workflow -> clean
• critical flake8 check from workflow -> clean

Notes

• Full-project Black/isort checks still report pre-existing formatting drift across many untouched files. The CI workflow treats these formatter/import checks as advisory (|| true / continue-on-error), and changed files were formatted with Black.

[github-actions]

🤖 Hi @newtontech, I've received your request, and I'm working on it now! You can track my progress in the logs for more details.