Release v1.9.0 model-family reliability

[docxology]

Summary

• Release v1.9.0 as the model-family reliability and interpretability release dated 2026-06-12.
• Make continuous and hierarchical Step 11/12 outcomes explicit manifest-profiled unsupported skips with concrete reasons, rather than raw failures accepted by profile math.
• Promote the model-family acceptance ledger/reporting evidence contract and update version, roadmap, changelog, README, and maintained evidence docs to the final measured counts.
• Harden analysis artifact provenance so isolated output runs cannot accidentally read stale tracked output/11_render_output simulation artifacts.

Validation

• git diff --check
• uv run --extra dev ruff check over changed Python files
• uv run --extra dev ruff format --check over changed Python files
• uv run --extra dev python doc/development/docs_audit.py --strict --check-anchors --no-write
• uv run --extra dev python scripts/check_gnn_doc_patterns.py --strict
• uv run --extra dev python scripts/check_maintained_doc_terms.py --strict
• uv run --extra dev python scripts/check_repo_terminology.py --strict
• uv run --extra dev python scripts/check_capability_contracts.py --strict
• uv run --extra dev python -m pytest src/tests/pipeline/test_model_family_acceptance.py src/tests/analysis/test_interpretability_summary.py src/tests/report/test_model_family_report.py src/tests/analysis/test_analysis_overall.py::TestAnalyzerSimulationMetrics -q -> 29 passed
• uv run --extra dev python scripts/run_model_family_acceptance.py --manifest input/model_family_manifest.json --output-dir /tmp/gnn-family-acceptance-all --strict -> passed, 9 families, continuous/hierarchical Step 11/12 profiled unsupported skips, no raw failed Step 11/12 counts
• uv run --extra dev python src/main.py --target-dir input/gnn_files/discrete --output-dir /tmp/gnn-v19-discrete-smoke --skip-steps "2" --skip-llm --verbose -> SUCCESS_WITH_WARNINGS, 23/23 selected steps successful, 0 failed
• uv run --extra dev python -m pytest --collect-only src/tests/ -q --tb=no --ignore=src/tests/llm/test_llm_ollama.py --ignore=src/tests/llm/test_llm_ollama_integration.py -> 2,399 collected tests
• uv run --extra dev python -m pytest src/tests/ -q --tb=no --ignore=src/tests/llm/test_llm_ollama.py --ignore=src/tests/llm/test_llm_ollama_integration.py -> 2381 passed, 17 skipped, 1 xfailed
• git diff --quiet -- output