docs: update README + add full MCP reference guide

README.md: - Updated Architecture section to reflect the full MCP stack - Replaced the 7-tool table with a complete MCP section: transports, tools (27), resources (20), prompts (6), agent workflow - Added Developer Tools section for typing_audit.py

docs/reference/mcp.md (new): - Full MCP 2025-03-26 reference: transports, auth, all 27 tools with parameter tables, all 20 resources, all 6 prompts with step-by-step workflows, error codes, 4 usage patterns, 3 Mermaid architecture diagrams