investigate

name	investigate
description	Phase 2 — Investigate candidate issues. Writes investigation.json next to each issue.json with evidence and a confirm/reject verdict.
user-invocable	true
allowed-tools	Bash, Read, Write, Edit, Glob, Grep, Agent

Phase 2: Investigation

Run from the repo root. The paper source is in this same repo.

Read .review/config.json to find the paper commit SHA and manuscript path.

Find candidate issues

Scan for all issue.json files that do NOT yet have an investigation.json next to them:

.review/chunks/<chunk-id>/<spotter>/issue.json    (from broad sweep)
.review/holistic/<slug>/issue.json                 (from holistic review)

Skip any directory that already has investigation.json (already investigated).

For each candidate issue

Use the investigate-issue sub-agent or investigate directly.

Manuscript investigation

• Grep for the key terms, symbols, and equation references mentioned in the issue
• Read related sections to check if the issue is addressed elsewhere (appendix, later section, footnote)
• Check cross-references and citations

Code investigation (if .review/config.json shows has_code: true)

• Read analysis scripts to verify claimed results
• Check parameter values in code vs. manuscript
• Run scripts if possible to reproduce numbers

Data investigation (if .review/config.json shows has_data: true)

• Verify sample sizes match claims
• Check that referenced data files exist

Write the verdict

Write investigation.json next to the issue.json (in the same directory). Never move or modify issue.json.

Confirmed:

{
  "verdict": "confirmed",
  "location": {"file": "<path>", "lines": [<start>, <end>]},
  "category": "<category>",
  "evidence": [
    {"searched_for": "<terms>", "scope": "<where>", "found": "<what>"}
  ],
  "suggested_fix": "<actionable suggestion>",
  "models_flagged": ["<model>"],
  "investigated_at": "<ISO timestamp>"
}

Rejected:

{
  "verdict": "rejected",
  "rejection_reason": "<concrete explanation with line numbers or code locations>",
  "investigated_at": "<ISO timestamp>"
}

Uncertain:

{
  "verdict": "uncertain",
  "notes": "<what was checked, why it's unclear>",
  "investigated_at": "<ISO timestamp>"
}

After completion

git add -A
git commit -m "review: investigation — <C> confirmed, <R> rejected, <U> uncertain"

Report: number confirmed, number rejected, brief summary of the most significant confirmed issues.