[codex] Sync student-facing Notebook 3 (GAMA)

[bernalde]

Closes #7.

Summary

This PR aligns the Python and Julia Notebook 3 materials at the student-facing level without moving logic out of the notebooks.

What Changed

• aligned the Notebook 3 teaching flow around the GAMA introduction, Graver basis introduction, problem statement, example, and the feasible-starting-point QUBO section
• added Python-side environment and execution notes near the notebook setup/import area
• added a shared references section to the Python notebook
• updated the Julia Notebook 3 metadata version so it matches the committed Julia environment
• added a Notebook 3 pair-sync test module that checks headings, setup guidance, references, and Julia metadata

Validation

• /home/bernalde/repos/QuIP/.venv/bin/python -m unittest tests.test_notebook3_pair_sync
• /home/bernalde/repos/QuIP/.venv/bin/python -m unittest discover -s tests
• ~/.local/bin/uv run --group docs python -m unittest discover -s tests

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[bernalde]

I reviewed the current PR head locally and ran:

/home/bernalde/repos/QuIP/.venv/bin/python -m unittest discover -s tests
~/.local/bin/uv run --group docs python -m unittest discover -s tests
QUIP_NOTEBOOK_TIMEOUT=3600 /home/bernalde/repos/QuIP/.venv/bin/python ./scripts/verify_notebooks.py notebooks_py/3-GAMA_python.ipynb notebooks_jl/3-GAMA.ipynb
make verify-julia-colab-smokes COLAB_JULIA_SMOKE_NOTEBOOKS=3-GAMA

The Python and docs unit suites passed, and the Julia Colab smoke passed. Direct execution of notebooks_py/3-GAMA_python.ipynb fails on the current head with ModuleNotFoundError: No module named 'Py4ti2int32', so I found two changes that should be made before merge and recorded them inline below.

[bernalde]

Follow-up on review #4094429003: both inline findings are fixed in 4cd43c2.

The Python Notebook 3 environment note now documents the local 4ti2 / Py4ti2 / Py4ti2int32 requirement in notebooks_py/3-GAMA_python.ipynb, and the pair-sync regression test now enforces that note in tests/test_notebook3_pair_sync.py.

I re-ran:
/home/bernalde/repos/QuIP/.venv/bin/python -m unittest tests.test_notebook3_pair_sync
/home/bernalde/repos/QuIP/.venv/bin/python -m unittest discover -s tests
~/.local/bin/uv run --group docs python -m unittest discover -s tests
make verify-julia-colab-smokes COLAB_JULIA_SMOKE_NOTEBOOKS=3-GAMA
QUIP_NOTEBOOK_TIMEOUT=3600 /home/bernalde/repos/QuIP/.venv/bin/python ./scripts/verify_notebooks.py notebooks_py/3-GAMA_python.ipynb notebooks_jl/3-GAMA.ipynb

The three Python test runs passed. The Julia smoke finished successfully, although it still emits the existing IJulia extension warnings in this environment. Direct local execution of notebooks_py/3-GAMA_python.ipynb still fails here on the external Py4ti2int32 dependency, which is why the note now calls that requirement out explicitly.

The remaining conversation comment on this PR is the ReviewNB bot message, which is informational only and did not require a code change.