Setup

Setup

Gets you from nothing to "agent searching my docs" in 60 seconds.

Usage

/gnosis:setup                      # Interactive — asks where your docs live
/gnosis:setup /path/to/docs        # Same, but ingest that folder right away
/gnosis:setup --postgres           # Print PostgreSQL setup instructions too

Target: $ARGUMENTS

Step 1 — Install

Pick the extras you need. They're additive.

pip install gnosis-mcp                        # core (SQLite, keyword search)
pip install 'gnosis-mcp[embeddings]'          # + local ONNX embeddings (hybrid search)
pip install 'gnosis-mcp[web]'                 # + web crawler (sitemap / BFS)
pip install 'gnosis-mcp[postgres]'            # + PostgreSQL backend
pip install 'gnosis-mcp[rst,pdf]'             # + .rst and .pdf file ingestion
pip install 'gnosis-mcp[reranking]'           # + cross-encoder reranker
                                              #   (OFF by default; tune before turning on —
                                              #    the bundled MS-MARCO model can HURT
                                              #    dev-doc retrieval by ~27 nDCG@10)

Full stack in one shot:

pip install 'gnosis-mcp[embeddings,web,postgres,rst,pdf]'

Verify:

gnosis-mcp --version     # should print the semver (≥ 0.10.13)

Step 2 — Pick a backend (usually SQLite)

SQLite (default): zero config. Database auto-creates at ~/.local/share/gnosis-mcp/docs.db. Great up to ~100 k chunks.

PostgreSQL: use when you have multiple concurrent writers, need a shared index across machines, or corpus > 100 k chunks.

# Postgres (only if you need it)
export GNOSIS_MCP_DATABASE_URL="postgresql://user:pass@localhost:5432/mydb"

Check that pgvector is available on the server:

psql "$GNOSIS_MCP_DATABASE_URL" -c "CREATE EXTENSION IF NOT EXISTS vector;"

Step 3 — Initialise the database

Idempotent. Safe to run any time.

gnosis-mcp init-db

Step 4 — Ingest your docs

If $ARGUMENTS includes a path, use it. Otherwise ask the user where their docs live.

# Preview (dry-run): lists files that would be ingested
gnosis-mcp ingest /path/to/docs --dry-run

# Real ingest, with embeddings for hybrid search
gnosis-mcp ingest /path/to/docs --embed

Default chunk size is 2000 characters (peak of the v0.11 sweep on real dev-docs). Tune it for your corpus with /gnosis:tune after you've got some real queries to score against.

Watch mode — auto re-ingests on file changes, no cron needed:

gnosis-mcp serve --watch /path/to/docs --transport streamable-http --rest

Step 5 — Verify

gnosis-mcp check     # DB connectivity + schema sanity
gnosis-mcp stats     # doc / chunk / embedding counts

Expect something like:

Backend:       sqlite
Version:       SQLite 3.46.0
chunks_table:  ✓ (1,742 rows)
fts_table:     ✓
sqlite_vec:    ✓ (1,742 vectors)
links_table:   ✓ (812 rows)

If anything says ✗, run /gnosis:status for diagnosis.

Step 6 — Wire your editor

Pick one. Each config goes in the project root (or global config — see each editor's docs).

Claude Code — .claude/mcp.json or ~/.claude/mcp.json

{
  "mcpServers": {
    "gnosis": {
      "command": "gnosis-mcp",
      "args": ["serve"]
    }
  }
}

For shared-state setups (agent teams, parallel tabs) — use HTTP:

{
  "mcpServers": {
    "gnosis": {
      "type": "url",
      "url": "http://127.0.0.1:8000/mcp"
    }
  }
}

Start the server separately:

gnosis-mcp serve --transport streamable-http --rest --watch ./docs

Cursor — .cursor/mcp.json

Same shape as Claude Code. Drop the JSON above.

Windsurf — ~/.codeium/windsurf/mcp_config.json

Same shape.

VS Code (GitHub Copilot) — .vscode/mcp.json

Key is "servers", not "mcpServers":

{
  "servers": {
    "gnosis": {
      "command": "gnosis-mcp",
      "args": ["serve"]
    }
  }
}

JetBrains — Settings → Tools → AI Assistant → MCP Servers

Command: gnosis-mcp, args: serve.

Cline — Cline's MCP panel in the sidebar

Command: gnosis-mcp, args: ["serve"].

Full per-editor guidance (including auth, env vars for write mode, and team / remote setups) lives in llms-install.md.

Step 7 — Report

Print a compact summary to the user:

## Setup complete

| Setting           | Value |
|-------------------|-------|
| Backend           | sqlite |
| Database          | ~/.local/share/gnosis-mcp/docs.db |
| Documents         | 42 |
| Chunks            | 170 |
| Embeddings        | 170 / 170 (100 %) |
| Chunk size        | 2000 chars (default) |
| Writable          | false (set GNOSIS_MCP_WRITABLE=true to enable upsert/delete) |

Next:
  /gnosis:search "your first query"   — sanity check retrieval works
  /gnosis:tune                         — find your chunk-size optimum (optional)
  /gnosis:ingest git <repo>            — index commit history too (optional)

Optional — extras

Git history

gnosis-mcp ingest-git . --since 6m --embed

Web crawl (vendor docs → local index)

gnosis-mcp crawl https://docs.stripe.com --sitemap --embed

Writes from your agent

Off by default for safety. Enable only if you want your agent to call upsert_doc / delete_doc:

export GNOSIS_MCP_WRITABLE=true

REST API on the same port

gnosis-mcp serve --transport streamable-http --rest

Then: curl http://127.0.0.1:8000/api/search?q=auth&limit=5.

Add Bearer auth for any non-localhost exposure:

export GNOSIS_MCP_API_KEY="$(python -c 'import secrets; print(secrets.token_urlsafe(32))')"

Notes

• Re-running ingest is cheap — content hashes skip unchanged files
• Watch mode beats cron — mtime polling + debounce, no fsnotify dep
• Rerankers are off by default: they help in some domains, hurt in others. Run /gnosis:tune full to find out which applies to your corpus before enabling
• PostgreSQL is a drop-in swap: set GNOSIS_MCP_DATABASE_URL and re-run init-db + ingest. Same tool API.