Lexomni MCP

MCP (Model Context Protocol) server for local knowledge management with Markdown and PDF indexing using SQLite FTS5.

Author: PagansDev (Paulo Gabriel Neves Santos) | Repository: github.com/PagansDev/lexomni-mcp

English

Usage

Requires Node.js 20.16 or newer.

As a local MCP server

1. Configure your MCP client (e.g., .mcp.json for Claude Code, .cursor/mcp.json for Cursor). Pin an exact version:

"lexomni": {
  "command": "npx",
  "args": ["-y", "[email protected]"],
  "env": { "LEXOMNI_WORKSPACE": "_lexomni" }
}

A relative LEXOMNI_WORKSPACE keeps a versioned config file portable across machines. Projects set up with @satlab/protocol get this entry from satlab-protocol init, and satlab-protocol update keeps it current.

2. Add your documents:

   • _lexomni/user/ - User markdown (guidelines, architecture, etc.)
   • _lexomni/agent/ - Agent notes (written by lexomni_writeNote)
   • _lexomni/books/ - PDFs (books, documentation, etc.)

3. Ask the agent to run lexomni_buildIndex. Searches only return what has been indexed.

How the workspace is resolved

1. LEXOMNI_WORKSPACE, when set. An absolute path is used as is; a relative one is resolved against the project root.
2. The project root is CLAUDE_PROJECT_DIR (set by Claude Code), otherwise the first root reported by the MCP client, otherwise the current directory.
3. Without LEXOMNI_WORKSPACE, the server looks for a _lexomni folder from the project root upwards and stops at the repository root (the first folder containing .git). If none is found, the workspace is <project root>/_lexomni.

Reading never creates folders: user/, agent/, books/ and index/ are created only when lexomni_writeNote or lexomni_buildIndex writes. lexomni_listSources and lexomni_searchDocs always report the workspace they used and return a warning when it is empty, when the index does not exist, or when it is out of date.

Available Tools

Agent handles parameters on its own

lexomni_listSources

Lists all documents (MD and PDF) in the workspace.

Parameters: none

Example:

{
  "workspace": "/path/to/project/_lexomni",
  "count": 5,
  "docs": [...]
}

lexomni_buildIndex

Indexes documents into SQLite FTS5 for fast search. This is the only tool that indexes, and it is incremental: documents whose size and modification time did not change are skipped, and documents removed from the workspace are dropped from the index.

Parameters:

• sources (optional): array of ["user", "agent", "books"]. Limits what is indexed and what can be removed.
• force (optional): reindex everything, changed or not.

Example:

{ "ok": true, "docsIndexed": 1, "indexed": 1, "skipped": 11, "removed": 0 }

lexomni_searchDocs

Keyword search across indexed documents. It never indexes: new or changed files appear only after the next lexomni_buildIndex, and the response carries a warning until then.

The query is literal text. Each word is matched as typed, so hyphens, quotes and colons are safe (third-party, CVE-2024-4367); FTS5 operators such as OR, NEAR or * are not interpreted.

Parameters:

• query (required): string, min 2 characters
• sources (optional): filter by source
• limit (optional): max results (1-50, default 10)

Example:

{
  "query": "clean architecture",
  "workspace": "/path/to/project/_lexomni",
  "hits": [
    {
      "docId": "user:user/guidelines.md",
      "chunkIndex": 0,
      "snippet": "...about [clean] [architecture]...",
      "source": "user",
      "relPath": "user/guidelines.md"
    }
  ]
}

lexomni_readDoc

• docId (required)
• Type: string Purpose: unique identifier of the document in the index.

Constraint: at least 3 characters. Typical source: taken from a hit returned by lexomni_searchDocs.

• chunkIndex (optional) Type: integer Minimum: 0 Purpose: which chunk (piece) of the document to read. If omitted: usually defaults to the first chunk (0), depending on implementation.
• maxChars (optional) Type: integer Range: 200–20000 Purpose: maximum number of characters of text to return for that chunk, useful to limit response size.

lexomni_writeNote

• filename (required) Type: string Purpose: name of the markdown file to create or update in the agent’s notes area.

Constraint: at least 1 character.

• content (required) Type: string Purpose: markdown content to write into the file.

Constraint: at least 1 character.

• mode (optional) Type: string Allowed values: "overwrite" – replaces the existing file content entirely. "append" – appends content to the end of the existing file. Default: "overwrite" if not specified.

Security

• Path traversal blocked (no ../, absolute paths or null bytes in note names)
• Write access limited to _lexomni/agent/, checked against the real path on disk
• Symbolic links are ignored when indexing and refused when writing notes, so a symlink inside the workspace cannot expose or overwrite files outside it
• PDFs are parsed only by lexomni_buildIndex, each one in a separate, sandboxed Node process (read-only access to the package and that PDF, no writes, no child processes, 100 MB / 512 MB / 60 s limits), with pdf.js string evaluation disabled
• Notes are limited to 1 MiB
• Runtime dependencies are bundled and releases are published from CI with provenance

See SECURITY.md for the supply chain policy, risky components and how to report a vulnerability.

Architecture

_lexomni/               # In user's project
  user/                 # Guidelines, architecture (read-only)
  agent/                # Agent notes (writable)
  books/                # PDFs (read-only)
  index/                # SQLite FTS5 (generated)
    lexomni.sqlite

Multilingual Strategy

Lexomni does not translate text internally. To find docs in PT and EN for e.g. :

1. Agent expands queries before searching:

   • "arquitetura em camadas" → also searches "layered architecture"
   • "fila" → also searches "message queue", "job queue"

2. Living glossary at _lexomni/agent/glossary.md:

   • Agent learns new terms via web search
   • Improves search quality over time

Development

npm run build      # Bundle into dist/ (index.js, pdf.worker.mjs, sql-wasm.wasm)
npm run dev        # Watch mode
npm start          # Run built server
npm test           # Tests
npm run lint       # Lint
npm run typecheck  # Typecheck

To run a local build from a clone, point the MCP client to it:

"lexomni-local": {
  "command": "node",
  "args": ["/path/to/lexomni-mcp/dist/index.js"],
  "env": { "LEXOMNI_WORKSPACE": "_lexomni" }
}

License

MIT © Paulo Gabriel Neves Santos