<!-- Author: Simon-Pierre Boucher — simon-pierre.boucher@uqo.ca -->
# Protocol-Guided Autonomous Research with Claude Code

**UQO Working Paper No. 29** — *Scientific Verification, Reproducibility, and the Cost of Delegation: A Controlled Study*

> A controlled, four-arm experiment in which fresh, isolated Claude Code sessions (bare mode, `claude-opus-5-5`) solve bounded scientific tasks under (A) an open instruction, (B) a structured research protocol, (C) the protocol plus controller-enforced executable gates, and (D) the same plus a separate review-and-repair session. Outcomes are scored by deterministic hidden oracles on a separate host. Every number in the paper is regenerated from `runs/state.sqlite`.

## Status
See `reports/phase_status.md` (append-only phase log), `protocol/amendments.csv` and `reports/interventions.csv`. The complete research mandate is `protocol/WP29_FULL_MANDATE.md`.

## Layout
```
protocol/        mandate, preregistration, contract, treatments (arms/), evaluation plan, screenshot protocol, amendments
research/        corpus of 11 source mandates (hashed), coding, literature matrix + verified BibTeX
configs/         budgets and per-split node/envelope configuration
tasks/           TASK_AUTHORING_SPEC.md, registry.csv, task_cards/, public_bundles/   (hidden oracles live in ~/wp29-oracles/, outside the repo)
src/pgar/        harness: contracts, state (SQLite), events, launcher (ssh + claude --bare), isolation, budgets, runtime_gates (gate program), recovery, scheduler, evaluation, exports, capture, evidence_viewer, cli
evaluators/      public receipt schema + run_validations.py (seeded evaluator validation)
tests/           infrastructure tests (no provider access)
runs/            state.sqlite + per-run directories (raw streams are not committed)
evidence/        screenshot originals (restricted, not committed) and public copies
analysis/        build_analysis_dataset, primary_analysis, robustness, figures, tables
results/         analysis_data (CSV exports), estimates, figures (PDF), tables (LaTeX)
paper/           LaTeX manuscript (UQO template)
reports/         environment/isolation audits, evaluator validation, pilot report, accounting, final review
```

## Commands (laptop = controller; see Makefile)
```bash
make test            # infrastructure tests (state machine, gate, evaluator, bundle hygiene)
make deploy          # install the gate program + key file on executor nodes
make probe           # sentinel isolation probes on the nodes (tiny live calls)
make smoke-live      # 1 task × 4 arms, live
PYTHONPATH=src .venv/bin/python -m pgar.cli assign --split pilot --tasks <ids> --repeats 1 --seed 202
PYTHONPATH=src .venv/bin/python -m pgar.cli run --split pilot --workers 8
make analyze && make paper
```
Requirements: Python 3.12 venv (`uv venv .venv --python 3.12 && uv pip install -p .venv/bin/python -e .`), SSH access to the executor nodes, `ANTHROPIC_API_KEY` in `~/wp29/.env` on each node, Claude Code 2.1.314 on the nodes.