{
  "artifact_path": ".reports/codex/research/<timestamp>/result.json",
  "checks_failed": [],
  "checks_run": [
    "lint",
    "format",
    "types",
    "tests",
    "review"
  ],
  "confidence": 0.0,
  "findings": {
    "critical": 0,
    "high": 0,
    "low": 0,
    "medium": 0
  },
  "metadata": {
    "confidence_gap_closures": [],
    "confidence_gaps": [],
    "confidence_recovery": {
      "evidence": [
        "objective source evidence"
      ],
      "final_confidence": 0.0,
      "initial_confidence": 0.0,
      "recovery_actions": [
        "recovery action"
      ],
      "remaining_limits": [
        "residual limit"
      ],
      "status": "shared-confidence-band-status"
    },
    "final_handoff": {
      "branch": "standard",
      "handoff_path": ".reports/codex/research/<timestamp>/final-handoff.json",
      "handoff_sha256": "sha256",
      "rendered_path": ".reports/codex/research/<timestamp>/final.md",
      "rendered_sha256": "sha256",
      "schema_version": 1,
      "validation_path": ".reports/codex/research/<timestamp>/final-handoff.validation.json"
    }
  },
  "schema_version": 2,
  "status": "pass|fail"
}

---
name: research
description: Research docs, papers, or state of the art; provide source-backed recommendations and caveats.
---

> Before asking, read [User Questions](../../shared/codex-user-questions.md).

# Research

Source-backed research for documentation, API migration, paper, or state-of-the-art questions.

## Input Schema

```json
{
  "question": "required research question",
  "mode": "docs|sota|paper|methodology|code-fidelity",
  "constraints": [
    "optional codebase, compute, version, or implementation constraints"
  ],
  "done_when": "recommendations are source-backed with caveats and confidence"
}
```

## Workflow

### 01: Create run directory

Run `create_run.py --skill research` per `../../shared/helper-cli-contract.md`.

### 02: Define research question, mode, and constraints

Modes:

- `docs`: current API/docs/migration answer.
- `sota`: method comparison and implementation recommendation.
- `paper`: single-paper analysis.
- `methodology`: experiment design, metric, guard, and ablation review.
- `code-fidelity`: compare paper/spec claims against implementation.

### 03: Gather sources

Write `<run-directory>/sources.md`:

```markdown
| Source | Type | Date/version | Why reliable | Used for |
| --- | --- | --- | --- | --- |
```

Source rules:

- Prefer primary docs, papers, specs, release notes, code.
- Use current live sources for volatile docs, dependencies, APIs.
- Mark stale/unavailable source explicitly.
- Never cite secondary summaries for high-impact claims unless independently corroborated.

For `sota`, `paper`, `methodology`, or `code-fidelity`, read and apply `../../shared/specialist-orchestration.md` only when independent expertise improves correctness; otherwise never load it. Write `<run-directory>/specialist-research-plan.md` with context packs for:

- `web-explorer`: current docs, release notes, API and dependency changes.
- `scientist`: formulas, methodology, metrics, ablations, benchmark claims.
- `solution-architect`: only when user expressly requests that advisory pass or selects the role for implementation fit, API boundaries, or migration shape; it returns a bounded read-only design artifact to the Sol parent/session for next action and acceptance.
- `squeezer`: performance or resource claims.
- `data-steward`: datasets, splits, leakage, reproducibility.
- `challenger`: unsupported recommendation or overconfident source synthesis.

Never send full papers, repositories, or all search results to every specialist. Give each only source excerpts, code files, questions needed for its axis.

### 04: Map to codebase context when implementation is relevant

Inspect `python PLUGIN_ROOT/shared/collect_diff.py --help`; collect `working-tree` scope into `<run-directory>/baseline`. Run topic scan separately; record unavailable paths/collection failures as evidence gaps.

**Structural context (optional)**: for `sota`/`code-fidelity` questions naming Python module/symbol, also probe codemap-py once: `python PLUGIN_ROOT/shared/codemap_adapter.py context --category analysis [--target <qname>] --out <run-directory>/codemap-context.json`. Per `../../shared/codemap-contract.md`, absence/incompatibility is non-fatal — continue with codebase mapping above. Persist result once here; any specialist context pack referenced in step 03 includes `<run-directory>/codemap-context.json`, never a fresh query — this artifact must exist before the step-03 dispatch wave fires, so produce it here in step 04 before that wave launches, not before step 03's own pack-construction text runs.

### 05: Produce `<run-directory>/research.md` with:

- `Question`
- `Constraints`
- `Source Table`
- `Findings`
- `Comparison` for SOTA/method choices
- `Implementation Fit`
- `Risks And Unknowns`
- `Recommendation`
- `Next Checks`

### 06: For paper/code-fidelity mode, include dimensions:

- `F`: formula/math match
- `H`: hyperparameter parity
- `E`: evaluation protocol
- `N`: notation and naming consistency
- `C`: citation/derivation chain

### 07: Run review gate

Run `git diff --check` as argv command. Write its combined output to `<run-directory>/review.txt` and retain its exit status as review evidence; never erase nonzero result.

### 08: Run shared gates and write the validated result artifact

Follow `../../shared/helper-cli-contract.md` and authoritative help. For research-only work, mark lint, format, types, tests inapplicable with concrete reasons; review requires non-empty `research.md`, `sources.md`, clean diff check. Write `RESEARCH_METADATA`, validate as `research`, promote only validated candidate.

Replace explicit skip with relevant command when research includes executable validation.

## Fail-Fast Rules

1. Missing question => fail.
2. No primary sources for high-impact/current claims => fail.
3. Recommendation not tied to constraints => fail.
4. Paper/code-fidelity claim without code or source reference => fail.
5. Result artifact missing => fail.

## Quality Gates

Required:

- `review`: source table, caveats, self-review, `git diff --check`.

Conditional:

- `tests`: when research includes executable validation or code-fidelity probe.

## Calibration Hooks

On source-protocol/recommendation-policy change, update calibration:

- behavioral cases: stale docs, unsupported SOTA claim, paper-code mismatch
- benchmark patterns: `research`

## Output Contract

Before writing result candidate, follow `../../shared/final-handoff-contract.md`: render and bind `final-handoff.json`, `final.md`, and `final-handoff.validation.json`; after both validators and promotion pass, emit `final.md` verbatim.

Use `../../shared/quality-gates.md`.

### Final chat

Final chat follows shared frame with `Next steps`. `Outcome`: recommendation/support level. `Results`: exactly `Recommendation | Evidence | Decision | Caveat / next check`, one row/recommendation. Include source freshness and each gap/caveat's next check.

Minimum artifact payload template: `result-template.json`.