Borrowing it
Nothing to install: this file belongs to alisoroushmd/zotero-mcp. Take a copy, put it at the same path in your own repository, and replace the rules that are about this project with yours.
curl -O https://raw.githubusercontent.com/alisoroushmd/zotero-mcp/main/AGENTS.mdgit clone --depth 1 https://github.com/alisoroushmd/zotero-mcpWrote 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/alisoroushmd/zotero-mcp/agents-md)<a href="https://agentmods.dev/instructions/alisoroushmd/zotero-mcp/agents-md"><img src="https://agentmods.dev/badge/instructions/alisoroushmd/zotero-mcp/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 | $0.05354 | $0.05354 |
| Opus 5 | $0.02677 | $0.02677 |
| Sonnet 5 | $0.01071 | $0.01071 |
| Haiku 4.5 | $0.00535 | $0.00535 |
Grade C, and why
zotero-mcp AGENTS.md scanned grade C with 1 finding 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 8d 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.
Hidden instructionshighPrompt injection
Directives inside HTML comments, invisible characters or bidirectional overrides are read by the model and not by the person reviewing the file.
<!-- SYNCED-FROM-CLAUDE source: /Users/ali.soroush/code/zotero-mcp/CLAUDE.md This file is a synced copy — edit the source, then re-run: bash /Users/ali.soroush/claude-memory/system/claude-port/sync_from_claude.sh --apply How it starts
The opening of the file, as written. The whole thing — 155 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Zotero MCP Server
MCP server for Zotero. Web API is the primary path for all operations. Local Zotero desktop API is an optional fast path for reads.
Commands
| Command | Description |
|---|---|
pip install -e ".[dev]" |
Install package + dev dependencies (editable) |
pip install -e ".[dev,graph]" |
Install with graph extras (networkx, numpy, scipy) |
pip install -e ".[dev,graph,fulltext]" |
Install with all extras (adds pypdf for PDF text extraction) |
python -m pytest tests/ -v |
Run all tests (mocked HTTP, no Zotero needed) |
python -m zotero_mcp |
Start MCP server (stdio transport) |
Architecture
src/zotero_mcp/
├── server.py # FastMCP tools + prompts — thin layer, delegates to clients
├── config.py # Centralized env var config (singleton, typed)
├── capabilities.py # Operating mode detection and status reporting
├── local_client.py # optional fast reads via localhost:23119 (Zotero desktop)
├── web_client.py # primary client: reads + writes via api.zotero.org
├── openalex_client.py # OpenAlex API — retraction checks, citation graph, bulk queries
├── citation_writer.py # .docx generation with Zotero field codes
├── graph_store.py # SQLite persistence for knowledge graph (papers, citations, entities, fulltext)
├── knowledge_graph.py # NetworkX graph analytics (PageRank, clusters, paths, temporal)
├── text_extractor.py # PDF text extraction via pypdf + FTS5 indexing
├── graph_renderer.py # D3.js HTML visualization of citation/author networks
└── semantic_scholar_client.py # Semantic Scholar recommendations (raw httpx)
Key Files
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.
- 8d ago First seen · 155 lines · 5,354 tokens per session scan C 0830de941265
zotero-mcp AGENTS.md is an instructions file published in the GitHub repository alisoroushmd/zotero-mcp (3 stars, last pushed 9d ago), licensed MIT. It adds 5,354 tokens to every session, about $0.0268 per session on Opus 5. A static security scan graded it C with 1 finding (hidden instructions). No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-31.
Other instructions, from other repositories
next.js AGENTS.md
AGENTS.md instructions for vercel/next.js, covering next.js development guide, codebase structure, monorepo overview, core package: packages/next and other important packages.
codex AGENTS.md
AGENTS.md instructions for openai/codex, covering rust/codex-rs, the codex-core crate, code review rules, crate api surface and model visible context.
vscode buildNext.instructions.md
Working notes and architecture documentation for the new esbuild-based build system in build/next. Use when making changes to the new build pipeline (transpile/bundle commands, NLS plugin, source-map handling, resource copying, or self-hosting watch tasks).
vscode oss-third-party-notices.instructions.md
Instructions for microsoft/vscode, covering vs code oss third-party-notices pipeline, architecture, pipeline flow in ci, applying the notice (cutover) and fallback chain (never fail the build).
langchain AGENTS.md
AGENTS.md instructions for langchain-ai/langchain, covering global development guidelines for the langchain monorepo, corridor security analysis, project architecture and context, monorepo structure and development tools & commands.
spec-kit AGENTS.md
AGENTS.md instructions for github/spec-kit, covering agents.md, about spec kit and specify, quickstart — add a new integration in 5 steps, integration architecture and integrationmanifest — file tracking.