feat: add MCP server for headless wiki operations (no Tauri/GUI)

[toughhou]

Summary

Adds a standalone MCP (Model Context Protocol) server that exposes llm_wiki's backend logic as AI-callable tools — without requiring the Tauri desktop app. This lets users give Claude Desktop, VS Code Copilot Chat, Cursor, or any MCP host direct access to their wiki knowledge base.

New: mcp-server/

mcp-server/
├── README.md          # Setup + Claude Desktop/VS Code config
├── package.json       # @modelcontextprotocol/sdk + graphology deps
├── tsconfig.json
└── src/
    ├── index.ts       # MCP server (stdio transport)
    ├── lib/           # Patched copies of graph-relevance, wiki-graph,
    │                  # graph-insights, search, path-utils
    ├── shims/
    │   ├── fs-node.ts        # Tauri IPC → Node.js fs drop-in
    │   ├── stores-node.ts    # zustand stores → module-level state
    │   └── embedding-stub.ts # Vector search stub (graceful degradation)
    └── types/wiki.ts

MCP Tools

Tool	Description
wiki_status	Page count + type breakdown
wiki_search	BM25 keyword search with optional RRF vector fusion
wiki_graph	Louvain community detection, JSON or summary format
wiki_insights	Surprising cross-community connections + knowledge gaps
wiki_lint	Orphaned pages, isolated nodes, structural issues

Quick Start

cd mcp-server && npm install && npm run build

# Claude Desktop: add to claude_desktop_config.json
# VS Code: add to .vscode/mcp.json
WIKI_PATH=/path/to/project node dist/index.js

Architecture Notes

The Tauri IPC boundary (@/commands/fs) is the only thing tying the TypeScript logic to the desktop app. The shims/fs-node.ts replaces all invoke() calls with standard fs module operations, making graph-relevance.ts, wiki-graph.ts, graph-insights.ts, and search.ts fully portable.

Works without Tauri: ✅ graph, search, insights, lint
Requires Tauri (not ported): ❌ ingest (PDF/DOCX extraction), deep-research (web fetch), sweep-reviews

Testing

cd mcp-server && npm install && npm run build

# Verify MCP protocol response
echo '{"jsonrpc":"2.0","method":"tools/list","id":1}' | node dist/index.js
# → Returns all 5 tools

# Test with real wiki
WIKI_PATH=/path/to/your/project node dist/index.js