Chore: add uv packaging and checkpoint hygiene

[annedranowski]

Summary

• normalize agent instructions into AGENTS.md and describe the emerging src/ architecture
• add pyproject.toml for uv-based setup while keeping requirements.txt synced with notebook/runtime dependencies
• add reusable local/GCS checkpoint helpers with run-date/run-id partitioning under gs://the-unknotters-checkpoints/upperbounds
• stop tracking generated output logs and ignore future output.txt, outputs/*.jsonl, and checkpoint outputs

Validation

• PYTHONPATH=src .venv/bin/python -m compileall -q src tests
• direct checkpoint assertion for gs://the-unknotters-checkpoints/upperbounds/run_date=2026-07-27/run_id=demo

Notes

• pytest is declared in the dev extra, but it is not installed in the current local venv, so direct assertions were used for local validation.