Add an MCP server contrib exposing the graph as native agent tools

Goal

Ship an MCP server under ./contribs/mcp_server that exposes the knowledge graph as native, callable agent tools — the "MCP server" row of the integration table in #10. This is step 2 of that issue's proposed plan (after the Skill), giving tool-native, cross-agent access (Claude Code, Cursor, etc.) with no Bash shell-out.

Tracks #10.

Why we are well positioned

The query layer is already "JSON in, JSON out" and the tool surface is effectively designed:

• GraphQuery (src/query/graph_query.ts) exposes instance methods that map one-to-one onto tools: whoCalls, references, blastRadius, deadExports, neighborhood.
• src/agent/agent_tools.ts already declares these as OpenAI-format function tools (find_symbol, who_calls, references, blast_radius, dead_exports, neighborhood). The MCP server is a thin re-expression of the same schema over the MCP protocol.

The hard part (a clean, machine-readable query surface) is done; this is plumbing.

Proposed tools

Scope

• New self-contained contrib package in ./contribs/mcp_server (its own package.json, following the web_visualisation contrib layout).
• Stdio MCP server (@modelcontextprotocol/sdk) that opens the graph database and adapts GraphQuery to MCP tool calls.
• Reuse the existing tool names/descriptions from agent_tools.ts so behavior matches the in-process agent.
• README with install snippet and the mcpServers config block for Claude Code / Cursor.

Out of scope

• The Skill (step 1 of #10) and the PreToolUse always-on hook (deferred in #10).
• Any change to core GraphQuery / extraction code — the adapter should be additive.

References

• Parent issue: #10
• GraphQuery: src/query/graph_query.ts
• Existing tool schemas: src/agent/agent_tools.ts
• Graphify MCP roadmap (their issue #146): https://github.com/safishamsi/graphify

Start by reading src/query/graph_query.ts and src/agent/agent_tools.ts, then compare the contribs/web_visualisation layout. The work is done when contribs/mcp_server contains its package, stdio MCP adapter, six matching tools, and README configuration examples, without changes to core GraphQuery or extraction code.