paper-synthesis

name	paper-synthesis
description	REQUIRED for any paper explanation or synthesis. Do NOT call attach_url_files and summarize inline — always use this skill. Use when given an arXiv URL, DOI, paper title, or Zotero reference.
metadata	{"short-description":"Summarize and explain research papers"}

Paper Synthesis (Main Agent)

You are an orchestrator. Spawn subagents to read papers, present results, persist to KB.

Your tools: exec_command, spawn_agent, wait, present_reading_view, update_document_section. Subagent-only (never call these): attach_url_files, crop_and_store_figure, paper_get.

The Flow

1. Resolve the paper — URL/ID/DOI directly. Only paper_search for bare titles. arXiv /abs/ → /pdf/. Zotero → $zotero.
2. KB check (skip if disabled) — rg "PAPER_ID" ${CODEX_KB_PATH}/cards/. If card exists, present it directly.
3. Spawn subagent — The subagent skill is paper-synthesizer (NOT paper-synthesis). Use exactly:

   spawn_agent(agent_type="synthesizer", message="$paper-synthesizer\n\nPaper: [URL]")
   

4. Wait — returns staging file path.
5. Read staging file — exec_command: cat [path].
6. Present — present_reading_view with headings, then update_document_section for each. Let the paper determine section names. Each section 15-30 lines, max 40, min 8. Include figures from staging file (![caption](path)) near relevant sections.
7. KB persist (skip if disabled) — write card via heredoc, append to journal, cleanup staging.
8. Cleanup — exec_command: for f in ${CODEX_KB_PATH}/staging/paper-*.md; do unlink "$f"; done

Multi-paper: Spawn in batches of 8 (system limit ~20 threads), one wait per batch. For KB, spawn fire-and-forget $kb subagent with all card contents.

Math

$...$ inline, $$...$$ display. Never backtick code spans for math — reading view renders LaTeX via KaTeX. Always blank line before list items.

KB Persistence

exec_command: cat <<'CARD_EOF' > ${CODEX_KB_PATH}/cards/paper-[slug].md
---
id: paper-[slug]
title: "[title]"
tags: [tags]
capsule: "[one-line summary]"
source: { type: paper, refs: ["[arXiv ID or DOI]"] }
status: current
date_added: [YYYY-MM-DD]
contributed_by: research-agent
---
[staging file body content]
CARD_EOF

Then append to research-journal.md and delete staging file. Follow-up persistence: spawn fire-and-forget $kb subagent when Q&A produces new insights. Card ID convention: paper-[kebab-case-slug].

Graceful Degradation

No KB: skip checks and persistence. PDF fails: synthesize from abstract. Title only: paper_search, ask for URL if not found. Subagent failures: present successful results, note failures.