docs: add Docker MCP Toolkit + SQLite MCP runbook

Adds docs/docker-mcp-sqlite.md, a reproducible recipe for installing the
SQLite MCP server into Docker MCP Toolkit so any connected MCP client
(Claude Code, Cursor, VS Code, etc.) gains six SQLite tools alongside
graphify's knowledge-graph tools.

Notes the catalog has two SQLite images at time of writing: `mcp/sqlite`
(marked Archived but works) and `mcp/sqlite-mcp-server` (broken
entrypoint). Recommends the working one.

Linked from README.md under a new 'Optional integrations' section.

This is unrelated to the upstream graphify pipeline; it lives as an
optional companion runbook for users who want a lightweight persistent
SQL workspace exposed to their MCP-aware AI clients.

Co-Authored-By: Oz <oz-agent@warp.dev>

README.md

@@ -426,6 +426,14 @@ Token reduction scales with corpus size. 6 files fits in a context window anyway
 
 graphify sends file contents to your AI coding assistant's underlying model API for semantic extraction of docs, papers, and images — Anthropic (Claude Code), OpenAI (Codex), or whichever provider your platform uses. Code files are processed locally via tree-sitter AST — no file contents leave your machine for code. Video and audio files are transcribed locally with faster-whisper — audio never leaves your machine. No telemetry, usage tracking, or analytics of any kind. The only network calls are to your platform's model API during extraction, using your own API key.
 
+## Optional integrations
+
+Runbooks for setting up extra tooling alongside graphify. None of these are required.
+
+| Integration | Doc |
+|---|---|
+| Docker MCP Toolkit + SQLite MCP server (lightweight persistent SQL workspace exposed to any MCP client) | [`docs/docker-mcp-sqlite.md`](docs/docker-mcp-sqlite.md) |
+
 ## Tech stack
 
 NetworkX + Leiden (graspologic) + tree-sitter + vis.js. Semantic extraction via Claude (Claude Code), GPT-4 (Codex), or whichever model your platform runs. Video transcription via faster-whisper + yt-dlp (optional, `pip install graphifyy[video]`). No Neo4j required, no server, runs entirely locally.

docs/docker-mcp-sqlite.md

@@ -0,0 +1,138 @@
+# Docker MCP Toolkit + SQLite MCP server
+
+A reproducible runbook for installing the **SQLite MCP server** into the
+[Docker MCP Toolkit](https://docs.docker.com/desktop/features/mcp/) so any
+connected MCP client (Claude Code, Claude Desktop, Cursor, VS Code, etc.) gains
+six SQLite tools: `read_query`, `write_query`, `create_table`, `list_tables`,
+`describe_table`, and `append_insight`.
+
+This document is *not* required to use graphify — it lives here as a known-good
+recipe for users who want a lightweight, persistent SQL workspace exposed to
+their AI clients alongside graphify's knowledge-graph tools.
+
+## Why SQLite (and not `sqlite-mcp-server`)
+At time of writing the catalog ships two SQLite MCP images:
+
+| Catalog name        | Image                  | Status |
+| ------------------- | ---------------------- | ------ |
+| `SQLite`            | `mcp/sqlite`           | Marked "Archived" in catalog metadata, but **boots and serves correctly** |
+| `sqlite-mcp-server` | `mcp/sqlite-mcp-server`| **Broken**: entrypoint `/app/.venv/bin/mcp-server-sqlite` does not exist in the published layer |
+
+Use `SQLite` (`mcp/sqlite`) until the newer image is fixed upstream.
+
+## Prerequisites
+- Docker Desktop running and healthy
+  - `docker info` returns a `Server Version`
+  - Public socket present at `/var/run/docker.sock` (or its symlink to
+    `~/.docker/run/docker.sock`)
+- Docker MCP Toolkit CLI plugin (`docker mcp`)
+  - Bundled with recent Docker Desktop releases; `docker mcp --version` should
+    print a version string
+
+## Install
+```bash
+# Add the working SQLite server to the default MCP profile
+docker mcp profile server add default \
+  --server catalog://mcp/docker-mcp-catalog/SQLite
+
+# Pre-pull the image so the first tool call is fast
+docker pull mcp/sqlite:latest
+```
+
+Verify the profile now contains both `fetch` (built-in) and `SQLite`:
+```bash
+docker mcp profile show default | grep -E '^[[:space:]]+name:'
+```
+
+Expected output:
+```
+            name: fetch
+            name: SQLite
+```
+
+The Docker MCP gateway should now expose 6 additional tools:
+```bash
+docker mcp tools count
+# → 15 tools (was 9 before adding SQLite)
+```
+
+## Smoke test
+The CLI can call MCP tools directly (each call boots a fresh gateway, ~5s
+overhead per call):
+```bash
+docker mcp tools call list_tables
+docker mcp tools call create_table \
+  query='CREATE TABLE IF NOT EXISTS notes (id INTEGER PRIMARY KEY AUTOINCREMENT, body TEXT NOT NULL, created_at TEXT DEFAULT CURRENT_TIMESTAMP)'
+docker mcp tools call write_query \
+  query="INSERT INTO notes(body) VALUES ('first row'), ('second row')"
+docker mcp tools call read_query \
+  query='SELECT * FROM notes ORDER BY id'
+docker mcp tools call describe_table table_name=notes
+docker mcp tools call append_insight insight='3 rows inserted; aggregates work.'
+```
+
+`read_query` should return the inserted rows with timestamps.
+
+## Storage layout
+Database file lives in a Docker named volume `mcp-sqlite`, mounted at `/mcp`
+inside containers:
+```
+mcp-sqlite (named volume) → /mcp/db.sqlite
+```
+
+Inspect from the host:
+```bash
+docker volume inspect mcp-sqlite
+docker run --rm -v mcp-sqlite:/mcp:ro alpine ls -la /mcp
+docker run --rm -v mcp-sqlite:/mcp:ro keinos/sqlite3 \
+  sqlite3 /mcp/db.sqlite '.schema'
+```
+
+The volume persists across `docker run --rm` invocations of the SQLite MCP
+container, so writes from one MCP tool call are visible to the next.
+
+## Wiring into MCP clients
+Connect once per client; the gateway exposes every server in the active profile:
+```bash
+docker mcp client connect claude-code   # already connected for many users
+docker mcp client connect cursor
+docker mcp client connect vscode
+docker mcp client connect claude-desktop
+# Supported: claude-code, claude-desktop, cline, codex, continue, crush,
+#            cursor, gemini, goose, gordon, kiro, lmstudio, opencode, sema4,
+#            vscode, zed
+```
+
+Verify wiring:
+```bash
+docker mcp client ls
+```
+
+## Uninstall / reset
+```bash
+# Remove server from the profile
+docker mcp profile server remove default SQLite
+
+# Drop the database volume (irreversible)
+docker volume rm mcp-sqlite
+
+# Remove the image
+docker rmi mcp/sqlite:latest
+```
+
+## Troubleshooting
+- **`starting client: calling "initialize": EOF`** — the requested server
+  failed its MCP handshake. Run the image directly to see the error:
+  ```bash
+  printf '{"jsonrpc":"2.0","id":1,"method":"initialize","params":{"protocolVersion":"2024-11-05","capabilities":{},"clientInfo":{"name":"smoke","version":"0.0"}}}\n' \
+    | docker run --rm -i -v mcp-sqlite:/mcp <image-ref> --db-path /mcp/db.sqlite
+  ```
+  Common causes: missing entrypoint binary in the image (the
+  `sqlite-mcp-server` failure mode) or missing required env/secrets.
+- **`cannot use --enable-all-servers with --servers flag`** — these gateway
+  args are mutually exclusive; pick one.
+- **No new tools appear in `docker mcp tools count` after install** — the
+  gateway may be running with `dynamic-tools` enabled, exposing only meta-tools
+  (`mcp-add`, `mcp-find`, …) until a profile is activated mid-session. Either
+  invoke `docker mcp tools` (which spins up an ephemeral gateway against the
+  default profile) or call `mcp-activate-profile` from inside an MCP session.