literature-review

name	literature-review
description	Write a literature review by iterating over papers one at a time, accumulating summaries and themes across iterations.

Shared files: progress.txt (done/remaining), learning.txt (cross-paper insights), research_note.md (summaries+themes), synthesis.md (final synthesis).

Lead Agent (loop controller — no reading/writing of papers)

1. Init (first run only): copy ./agents/skills/templates/{progress,learning,research_note,synthesis}.* into working dir if not exist. List all PDFs; populate progress.txt with unchecked entries.
2. Spawn Abstract Extraction Sub-Agent per paper in parallel via Task tool. Wait for all.
3. Spawn Planning Sub-Agent once. Wait.
4. Spawn Reading Sub-Agent for next unreviewed paper. Wait. Repeat until all done.
5. Spawn Synthesis Sub-Agent once. Then stop.

Sub-Agents (all spawned via Task tool, general/mode: subagent)

Abstract Extraction (parallelizable, once per paper):

1. Run uv run python3 tools/extract_pdf.py <input.pdf>.
2. Append filename.pdf: abstract text to abstracts.txt. Append only; do not read.

Planning (once):

1. Read abstracts.txt.
2. Reorder progress.txt entries foundational-first. Do not mark any paper done.

Reading (sequential, once per paper):

1. Read progress.txt → pick next unreviewed paper.
2. Read learning.txt for accumulated themes/gaps.
3. Extract paper: uv run python3 tools/extract_pdf.py <input.pdf>.
4. Read templates/research_note.md for format; append new entry to research_note.md. Append only; do not read research_note.md.
5. Append to learning.txt (format from templates/learning.txt). Note contradictions; avoid restating existing themes.
6. Mark paper done in progress.txt with one-line note.

Synthesis (once, after all papers done):

1. Read research_note.md and learning.txt.
2. Read templates/synthesis.md for format.
3. Overwrite synthesis.md with all three sections: Synthesis, Contradictions, Open Questions.

Writing style (all sub-agents):

• concise by sacrificing grammer but avoid ambiguity
• define jargon
• LaTeX for equations (display mode for key ones)
• max 3 sentences/paragraph
• paragraph-based narrative
• no bullets/tables
• conversational tone

Writing style (learning.txt):

• speak aloud your thought process as you read each paper.
• keep the reflection conncise and focused on insights/themes/gaps.
• if any issue in tool usage, note it here and move on.

Stop Conditions

• All papers reviewed + synthesis.md written
• Sub-agent fails repeatedly → escalate to user
• User cancels