Extend first run setup staleness checks and docs

[jmsexton03]

Summary

Related or overlapping functionality / DRY guidance

• What other functionality overlaps this change, and can it be reused to avoid duplication?
• If adding a non-optional variable or function argument (esp. node updates), how does that align with src/models/graph_state_canonical.py and the written node contracts in tests/contracts?
• Does this decrease pytest coverage or add tests in tests/unit or tests/integration?
• This embeds a significant architectural decision that needs an ADR.
  • If checked, add an ADR under docs/adr/ (one short file describing context, decision, consequences).

Impact checklist

• fixes a bug or incorrect behavior
• adds new capabilities
• changes answers in the test suite to more than roundoff level
• likely affects downstream users or results
• includes docs updates (code/docs), if appropriate
• none of the above

Tests run (CI runs: pytest tests/unit, pytest tests/quality, pytest tests/integration -m "integration_l1 or integration_l2 or integration_l3 or integration_l4 or integration_full")

• tests/unit: pytest tests/unit
• tests/quality: pytest tests/quality
• integration ladder (CI): pytest tests/integration -m "integration_l1 or integration_l2 or integration_l3 or integration_l4 or integration_full"
• other (list):
• Output/summary:
• If tests require repos/schemas/indices or real services, note markers used.
• requires_solver(...) implies repo + schema + default indices are available locally.
• Use -k pelec|erf|amrex|warpx to filter solver-specific tests.

Examples:

pytest tests/unit --tb=short -q
pytest tests/quality --tb=short -q
pytest tests/integration -m "integration_l1 or integration_l2 or integration_l3 or integration_l4 or integration_full" --tb=short -q
pytest -m "e2e and demo" tests/e2e/test_demo_smoke.py --tb=short -q

Tests not run in CI (required if any)

• CI runs tests/unit, tests/quality, and tests/integration with integration_l1..l4 + integration_full markers via micromamba; list anything else not covered by CI here.
• None
• tests/e2e
• other (list):
• Reason for skip:
• Risk/mitigation:

API-key/manual tests (optional, include steps)

• Env vars or credentials needed:
• Manual steps/commands:
• Results or logs:

Integration/E2E markers (optional, manual, may require API key)

• Note: integration ladder runs in CI; tests/e2e runs only when selected by path or -m e2e.
• e2e demo (workflow_dispatch): pytest -m "e2e and demo" tests/e2e/test_demo_smoke.py
• other (markers: use_real_services, requires_repos, requires_schema):

Notes (optional)

• Manual output / logs (short):
• Known limitations:

Labels (optional)

• I will check auto-labels after submitting.
• Labels are okay if slightly off.

Maintainability note (optional)

• Prefer the most maintainable, DRY, and human-readable option; add duplication only with a clear reason.