Agent harness for research: literature review

mkdir -p sources/txt notes out
for f in sources/*.pdf; do
  pdftotext -layout "$f" "sources/txt/$(basename "${f%.pdf}").txt"   # poppler-utils
done

# Literature review rules
- Sources live in `sources/txt/`. Never edit anything in `sources/`.
- Write one notes file per source to `notes/<source>.md`.
- Every claim in notes or the brief needs a citation: (file, page).
- Quote exactly when a number or definition matters. No paraphrased numbers.
- If a source doesn't say it, write "not stated". Never fill gaps from memory.
- The final brief goes to `out/brief.md`: findings, disagreements, open questions.

---
name: reader
description: Reads ONE source file and writes structured, cited notes. Use once per source.
tools: Read, Grep, Glob, Write
model: inherit
---
You read exactly one file from sources/txt/ and write notes/<same-name>.md with:
1. Question and method (2-3 lines)
2. Key findings, each with (file, page)
3. Exact quotes for every number
4. Limitations the authors state
Write "not stated" for anything missing. Never use outside knowledge.

{
  "permissions": {
    "deny": ["Edit(sources/**)"]
  }
}

claude "Use the reader subagent on each file in sources/txt/, then write out/brief.md from notes/ following AGENTS.md"

version: "1.0.0"
title: "Literature review"
description: "Cited brief from a folder of text sources"
parameters:
  - key: topic
    input_type: string
    requirement: required
    description: "Question the brief should answer"
  - key: folder
    input_type: string
    requirement: optional
    default: "sources/txt"
    description: "Folder of .txt sources"
instructions: |
  Follow AGENTS.md. Read every file in {{ folder }} one at a time and write
  notes/<file>.md with (file, page) citations. Then write out/brief.md
  answering: {{ topic }}. Write "not stated" instead of guessing.
prompt: "Start the review."

goose run --recipe review.yaml --params topic="What changed in agent evals this month?" --max-turns 40