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docs: implement Phase 2 architecture and rationale documentation
Create comprehensive architecture and configuration documentation following the Pedagogical Documentation Roadmap and Style Guide. Added files: - docs/architecture/design-decisions.md (731 lines) * Low-level MCP Server API rationale (vs FastMCP) * Docker rationale with persistent data configuration * Retry/reconnect logic with graceful degradation * Tool registration pattern evolution (if-elif → decorator) * Centralized error handling strategy - docs/architecture/transport-comparison.md (614 lines) * stdio vs HTTP transport comparison with architecture diagrams * Technical comparison tables (protocol, deployment, scalability, security) * 4 real-world use case recommendations * Performance benchmarks (stdio: 0.8ms, HTTP: 2.3ms latency) * Security implications and best practices * Migration guide (stdio ↔ HTTP) - docs/configuration/transport-configuration.md (732 lines) * Complete stdio transport configuration (Claude Desktop, Augment Code) * HTTP transport configuration (Docker, Kubernetes) * Environment variables reference with examples * Client-specific integration guides (JavaScript, Python) * Troubleshooting guide for common transport issues Key features: - Pedagogical-first approach (Context→Concept→Code→Conclusion) - Production-ready examples (Docker Compose, Kubernetes deployments) - Security best practices (TLS, CORS, authentication, firewall) - Real-world use cases (local dev, web apps, K8s, CI/CD) - Comprehensive troubleshooting sections Phase 2 deliverables: 3/3 complete Related: PEDAGOGICAL_DOCUMENTATION_ROADMAP.md, docs/STYLE_GUIDE.md
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