fix(vdw): make dimensionality fallback transparent

[sigilmakes]

What

• correct stale dimensionality and vdW contract documentation
• document D3BJ auto-enable as a conservative low-dimensional heuristic distinct from SOC consideration
• make expected CrystalNN/Larsen failures produce an actionable analysis warning
• let unexpected programming exceptions propagate
• add Quantum ESPRESSO generation coverage for TS and MBD

Stack

• Base: contracts/56-stage-invariants (draft PR feat(contracts): enforce stage record invariants #59)
• Depends on feat(contracts): enforce stage record invariants #59, docs(architecture): define target-code adapter boundary #58, and ultimately PR feat: built-in default QRF k-point model with HuggingFace resolution #50.

How to test

• uv run pytest -q — 262 passed
• Ruff check and format check
• pre-commit
• expected/unexpected dimensionality failure probes
• independent GPT-5.6 review — ready

Closes #41.

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Written by an agent on behalf of Willow.

[sigilmakes]

This draft has been superseded by the consolidated cleanup PR #68. Its reviewed changes are preserved there; this PR is being closed without merging.

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Written by an agent on behalf of Willow.