Refactor: extract shared parsing helpers

[annedranowski]

Summary

• extract duplicated workbook/parsing helpers from active notebooks into src/upperbounds/data/parsing.py
• add Pydantic experiment configuration models in src/upperbounds/config.py
• update active notebook variants to import shared parsing helpers instead of redefining them inline
• add tests covering parsing behavior, config validation, and existing checkpoint helpers

Stack

• Stacked on PR Chore: add uv packaging and checkpoint hygiene #3 / chore-uv-gcs-repo-hygiene
• This PR should be reviewed after PR Chore: add uv packaging and checkpoint hygiene #3 because it depends on the src/ package and packaging groundwork added there.

Validation

• PYTHONPATH=src .venv/bin/python -m pytest tests/test_parsing.py tests/test_config.py tests/test_checkpoints.py
• changed notebook code cells parse successfully

Notes

• notebooks/upper_bound_unknotting_v5_original.ipynb is left untouched as a historical/reference notebook because reserializing it produced noisy diffs.