template-reproducibility-audit

# Reproducibility audit Complements [manuscript-claim-verification](../manuscript-claim-verification/SKILL.md) (claim truth) by focusing on **stability of artifacts**. ## Natural invoke - "Prove template_code_project is reproducible before Zenodo" - "Numbers in the PDF don't match after a clean rebuild" - "Double-run the pipeline and diff outputs" ## Inputs to confirm - **Project** — from [`docs/_generated/active_projects.md`](../../_generated/active_projects.md). ## Workflow 1. **Determinism** — fixed RNG seeds, `MPLBACKEND=Agg`; no wall-clock/hostname/path leaks. List nondeterministic sources. 2. **Regenerate from clean** — wipe working outputs, run core pipeline, regenerate manuscript variables. Capture exit status per stage. 3. **Diff** — compare regenerated `output/<name>/` and manuscript variables vs prose assertions. Hand-typed numbers not from generated variables are findings even if equal. 4. **Double-run stability** — regenerate twice with clean tree between; any run-1 vs run-2 diff is hard failure. 5. **Fix** — seed injection, variable-ize hard-typed numbers, remove timestamp leakage. Update `projects/<n>/AGENTS.md` and README.md with regeneration command. Never hand-edit `output/`. ## Deliverables - Drift table: artifact | committed | regenerated | action. - Commands + raw output; no invented coverage numbers. ## Verification commands ```bash uv sync uv run python scripts/runner/execute_pipeline.py --project <project> --core-only uv run python proje...