docs: add layered architecture and abdominal pain flow guide

[lobokiol]

Summary

• add a dedicated architecture document describing the proposed presentation -> application -> domain -> infrastructure -> mcp_servers layering
• map the target layering to the repository's current app/api, app/graph, app/domain, app/mcp, and app/infra layout
• include Mermaid diagrams for the layered architecture, dependency direction, target directory design, and the business flow for 我肚子疼，该怎么办
• link the new document from the README so it is discoverable from the repository homepage

Validation

• git diff --check
• no automated tests run (documentation-only change)