Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx agentmods add instructions/aytzey/paper-pilot/agents-mdgit clone --depth 1 https://github.com/aytzey/paper-pilotWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/instructions/aytzey/paper-pilot/agents-md)<a href="https://agentmods.dev/instructions/aytzey/paper-pilot/agents-md"><img src="https://agentmods.dev/badge/instructions/aytzey/paper-pilot/agents-md.svg" alt="Measured on agentmods" height="20"></a>What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.01073 | $0.01073 |
| Opus 5 | $0.00536 | $0.00536 |
| Sonnet 5 | $0.00215 | $0.00215 |
| Haiku 4.5 | $0.00107 | $0.00107 |
Grade A, and why
paper-pilot AGENTS.md scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 5d ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
How it starts
The opening of the file, as written. The whole thing — 107 lines — stays where its author put it; the contents beside it link to each section on GitHub.
AGENTS.md
This file is the shared entry point for any coding or research agent working with paper-pilot.
What This Repository Does
This project exposes an MCP server for:
- academic search across 6 databases (Semantic Scholar, OpenAlex, arXiv, Crossref, Europe PMC, DOAJ)
- open-access PDF resolution and inspection
- Sci-Hub paper resolution and download (opt-in, disabled by default)
- deep reading with full-text extraction and chunking
- PDF page rendering for charts, tables, and figures
- interactive citation/relatedness graph export (HTML)
- Zotero sync in both local and web modes
There is also a zero-config CLI: paper-pilot demo "<topic>" runs the whole pipeline and opens a citation graph without any MCP client.
Read Order
If you need context fast, read files in this order:
- README.md
- docs/ARCHITECTURE.md
- src/paper_pilot/server.py
- src/paper_pilot/services/zotero.py
- CLAUDE.md or CODEX.md, depending on the client
Recommended Tool Order
For most research tasks, use tools in this order:
healthcheckresearch_topicfor broad discovery and report generationdeep_read_topicwhen you need evidence chunks and local PDF accessrender_pdf_pageswhen visual inspection matters (returns the pages as images you can see)read_pdf_documentto get a downloaded PDF's local path + resource link (pass embed_base64=true only if your client reads inlined PDFs)get_pdf_page_textto pull the exact text of specific pages (a reference, a table) when you cannot read the file from diskgraph_topic(orwrite_graph=True) when a citation/relatedness map helpslist_zotero_collectionsbefore writing into an existing collection
Use search_literature and find_similar_papers when you want fine-grained control instead of the bundled pipeline.
Important Output Locations
The server writes artifacts under data/:
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 5d ago First seen · 107 lines · 1,073 tokens per session scan A 4053089bf388
paper-pilot AGENTS.md is an instructions file published in the GitHub repository aytzey/paper-pilot (12 stars, last pushed 1mo ago), licensed MIT. It adds 1,073 tokens to every session, about $0.0054 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.
Other instructions, from other repositories
mcp AGENTS.md
Instructions for SpaceFrontiers/mcp, covering agents.md — space frontiers mcp server, what it does, layout, local dev and conventions.
easy-notion-mcp CLAUDE.md
Claude Code instructions for Grey-Iris/easy-notion-mcp, covering easy-notion-mcp, open source context, .meta/ publication policy (hybrid, 2026-07-02), standing priorities and commands.
adeu GEMINI.md
Gemini CLI instructions for dealfluence/adeu, covering adeu — native track changes for ai, available tools, readdocx, processdocumentbatch and applytextrevision.
Guanlan CLAUDE.md
Instructions for shenyangs/Guanlan, covering claude.md, project, durable memory surfaces, development commands and core structure.
openings-mcp AGENTS.md
Instructions for amikai/openings-mcp, a project described as: 💼 One MCP server to search job boards and company career sites.
MCP-Airflow-API copilot-instructions.md
Instructions for call518/MCP-Airflow-API, covering copilot instructions for mcp-airflow-api, project architecture, critical patterns, functions.py - persistent session with retry strategy and standard pattern in airflowapi.py.