docs: update Architecture.md for api-server + mcp-transport split

Rewrite architecture document to reflect the package split:
- Describe both packages with clear ownership boundaries
- Add detailed file listings for mcp-transport (tools, schemas, auth, config)
- Update dependency flow diagram to show transport → API → DB chain
- Update all development commands (api:dev, mcp:stdio, etc.)
- Update testing commands for both packages
- Split environment variables by package
- Add changelog entry for the February 2026 split

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Author: PaulJPhilp