deduplicate

name	deduplicate
description	Phase 3 — Deduplicate confirmed issues by writing a dedup.json mapping file. No files are moved or modified.
user-invocable	true
allowed-tools	Read, Write, Glob, Grep

Phase 3: Deduplication

Run from the repo root. Requires investigated issues from Phase 2.

Process

1. Scan for all directories that have both issue.json and investigation.json with "verdict": "confirmed" (or "uncertain").

2. For each confirmed issue, read issue.json (title, quoted_text, description, spotter) and investigation.json (location, category).

3. Cluster by:

   • Location proximity: issues referencing lines within +/-10 lines of each other in the same file
   • Topic similarity: issues about the same symbol, equation, or claim
   • Same spotter on overlapping chunks: the same spotter firing on adjacent chunks likely found the same issue

4. For each cluster, pick a canonical representative (the one with the best evidence or most specific location).

Output

Write a single file: .review/dedup.json

{
  "clusters": [
    {
      "canonical": "chunks/intro-00-a3f2bc/undefined_symbols",
      "members": [
        "chunks/intro-00-a3f2bc/undefined_symbols",
        "chunks/intro-01-b7c1de/undefined_symbols"
      ],
      "reason": "Same issue: undefined kappa, overlapping chunks"
    },
    {
      "canonical": "holistic/missing-robustness",
      "members": ["holistic/missing-robustness"],
      "reason": "Singleton"
    }
  ],
  "cross_references": {
    "chunks/model-00-c4d5/methodology_errors": ["chunks/results-00-e6f7/overclaiming"]
  }
}

Important: Paths in dedup.json are relative to .review/. The canonical path is used by downstream phases to identify which issues to process.

Do NOT modify or move any issue.json or investigation.json files. The dedup mapping is a separate overlay.

After completion

git add -A
git commit -m "review: deduplication — <N> canonical issues from <M> total confirmed"

Report: how many canonical issues remain, how many were merged, how many have cross-references.