MCP server

LLM-driven drafting workflows are the new pressure point for citation handling. The model proposes a passage, the author asks “where’s that from?”, and someone — model or human — fills in a reference. Today the model hallucinates the DOI, links to whatever URL appears in its training data, or breaks the loop and dumps the work in the author’s lap.

Manubot solves exactly this problem (resolve doi:, pmid:, arxiv:, isbn:, url:, wikidata:, pmc: keys to canonical metadata via the source APIs) and has been doing it for eight years — but only inside its own pandoc filter. An agent calling out from Claude Desktop, Codex, or Gemini Code Assist can’t reach it.

quartobot mcp closes that gap. It starts a stdio MCP server that hands the agent three read-only tools backed by the same code the CLI uses for the pre-render hook. Eight years of accumulated source-API bug fixes show up as one primitive in the agent’s toolkit; nobody has to reimplement them.

Install

The server ships as an opt-in extra. Base quartobot installs don’t pull the MCP SDK.

uv tool install 'quartobot[mcp]'

If quartobot is already installed without the extra, re-running with [mcp] upgrades in place. Confirm:

quartobot mcp --help

Tools

The server registers three tools. All are read-only — nothing writes to your filesystem.

resolve_citation(cite_key)

Resolve a single persistent-identifier key to CSL JSON. Direct wrap of manubot.cite.citekey_to_csl_item — same resolver quartobot resolve uses, same metadata.

Accepts a leading @ and trailing pandoc-terminator punctuation (/, ., ,, etc.); both are normalized away. Errors return as a {"error": ..., "cite_key": ...} dict rather than crashing the server, so an agent can recover and explain the failure.

scan_project(path, recursive=true)

Walk a Quarto project directory and return the cite-key inventory grouped by prefix, plus per-key occurrence locations. Same scan quartobot scan does. Useful when the agent needs to see what’s already cited before proposing a new reference.

validate_project(path)

Run the same pre-flight checks quartobot validate runs: _quarto.yml exists and declares bibliography:, project.pre-render calls quartobot resolve --id-mode citation-key, references.json is in the bibliography list, no duplicate cite keys across files. Returns the full check list, a passed boolean, and the failures separately. Useful for an agent confirming its edits don’t break the manuscript’s CI gate.

Client setup

All examples assume quartobot is on the shell PATH (the uv tool install path puts it there). Stdio transport only — no port to configure, no auth to wire up.

Claude Desktop

Edit ~/Library/Application Support/Claude/claude_desktop_config.json (macOS) or %APPDATA%\Claude\claude_desktop_config.json (Windows):

{
  "mcpServers": {
    "quartobot": {
      "command": "quartobot",
      "args": ["mcp"]
    }
  }
}

Restart Claude Desktop. The three tools show up under the MCP icon at the bottom of the chat input. Test with: “use quartobot to resolve doi:10.1371/journal.pcbi.1007128.”

Codex CLI

Codex reads MCP servers from ~/.codex/config.toml. Append:

[mcp_servers.quartobot]
command = "quartobot"
args = ["mcp"]

Restart any running Codex session. The tools become available to the agent automatically.

Gemini Code Assist (VS Code)

Open the workspace’s .vscode/settings.json (or your user settings) and add:

{
  "geminicodeassist.mcpServers": {
    "quartobot": {
      "command": "quartobot",
      "args": ["mcp"]
    }
  }
}

Reload the window. Gemini sees the tools on its next call.

Any other MCP client

Same command pattern. The server speaks plain stdio MCP, so any client that lets you point at a binary works:

command: quartobot
args: ["mcp"]

What’s not here

• No write tools. No init, no scaffolding, no auto-write to _quarto.yml. The cost of a hallucinated citation is small and scoped to the agent’s reply; the cost of an agent writing a scaffold into the wrong directory is not. If MCP grows a confirmation-UX primitive that the major clients honor, that calculus changes.
• No HTTP/SSE transport. Every authoring client that matters today is stdio. The MCP spec supports networked transports; quartobot mcp doesn’t, until somebody asks.
• No quartobot mcp install <client> helper. Each client has its own config schema and filesystem layout; chasing the drift on three or four moving targets is the kind of maintenance load that outweighs the convenience. The snippets above are short enough.