refactor: extract shared invariant helpers

[annedranowski]

Summary

• Extracts shared Jones polynomial and invariant helpers from duplicated notebook code into reusable Python modules.
• Updates notebooks to import the shared invariant logic instead of maintaining repeated local copies.
• Keeps this PR stacked on refactor/shared-src-layout so the diff remains reviewable.

Validation

• Parsed edited notebooks for Python syntax.
• Ran focused shared-module tests with PYTHONPATH=src .venv/bin/python -m pytest tests/test_invariants.py tests/test_parsing.py tests/test_config.py tests/test_checkpoints.py tests/test_paths_workbook_targets.py.