Doctree MCP server

doctree-mcp

Agentic document retrieval over markdown, CSV, and JSONL. BM25 + tree navigation via MCP — no vector DB, no embeddings, no LLM calls at index time.

The pitch: MCP provides the structural primitives (a navigable tree, BM25, glossary, row lookup). The bundled skills provide the procedural knowledge (how to walk that tree). Together the agent behaves like a trained research librarian — not a one-shot searcher. See The Skill + MCP Pattern.

Quick Start

Have docs already? Point a client at them:

# In your AI tool's MCP config — see docs/CLIENTS.md for per-tool snippets
{ "mcpServers": { "doctree": {
    "command": "bunx", "args": ["doctree-mcp"],
    "env": { "DOCS_ROOT": "./docs", "WIKI_WRITE": "1" }
} } }

Restart the tool → ask "search the docs for X" or invoke the doc-read prompt.

Starting fresh? Scaffold a Karpathy-style LLM wiki:

bunx doctree-mcp init          # configure current tool
bunx doctree-mcp init --all    # configure every supported client
bunx doctree-mcp init --dry-run

Creates docs/wiki/ (LLM-maintained) + docs/raw-sources/ (your inputs), writes the MCP config, installs a post-write lint hook, appends wiki conventions to CLAUDE.md / AGENTS.md / .cursor/rules/.

Operation Modes

Full decision tree: Operation Modes.

How It Works — Retrieve · Curate · Add

Agent: "How does token refresh work?"

→ search_documents("token refresh")
  #1  auth/middleware.md § Token Refresh Flow       score: 12.4
  #2  auth/oauth.md       § Refresh Token Lifecycle  score: 8.7

→ get_tree("docs:auth:middleware")
  [n1] # Auth Middleware
    [n4] ## Token Refresh Flow
      [n5] ### Automatic Refresh

→ navigate_tree("docs:auth:middleware", "n4")   ← n4 + descendants

Core read tools (always on):

Wiki write tools (opt-in with WIKI_WRITE=1):

Safety: path containment · frontmatter validation · duplicate detection · dry-run · overwrite protection.

Deprecated aliases (listdocuments, findfiles, findsymbol) are superseded by searchdocuments — still functional, no longer recommended.

The Skill + MCP Pattern

Most retrieval tools hand the agent a search box and hope for the best. doctree-mcp hands it a tree, and the bundled skills teach it how to walk one.

• MCP = structural primitives. searchdocuments, gettree, navigatetree, getnodecontent, lookuprow return tree positions the agent reasons over — not finished answers.
• Skills = procedural knowledge. /doc-read, /doc-write, /doc-lint encode breadcrumb drill-down: search → outline → navigate → retrieve. The agent learns the policy, not just the API.

That pairing doesn't exist cleanly elsewhere:

Shortened. The full README is on GitHub.