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)