feat: implement protocol extensions and observability features

[Copilot]

Why?

Addresses #5 - adds MCP protocol capabilities (tools, notifications, sampling) and operational observability to the SDD server.

What Changed?

New modules:

• mcp_server/tools.py - Helper tools for workspace operations:
  • list-artifacts - enumerate specs/tasks
  • create-spec-stub - generate spec files with auto-numbering
  • summarize-diff - text comparison summaries
• mcp_server/notifications.py - broadcasts workspace file events via send_resource_list_changed()
• mcp_server/sampling.py - requests client-generated summaries/analysis via MCP sampling protocol
• mcp_server/logging.py - structured JSON/text logging + health checks

Health endpoints:

• GET /health - simple liveness check
• GET /mcp/health - detailed readiness with workspace/prompts status, returns 503 on degraded

Integration:

• Registered all tools in mcp_server/__init__.py via FastMCP decorators
• Tools discoverable via FastMCP Inspector

Test coverage:

• 32 new tests in tests/test_tools_protocol.py covering tools, notifications, sampling, logging
• All 111 tests pass, 83% coverage maintained

Documentation:

• Updated docs/operations.md with observability section including health endpoint examples, structured logging config, and helper tool reference

Additional Notes

Environment variables for logging control:

• SDD_LOG_LEVEL - DEBUG/INFO/WARNING/ERROR (default: INFO)
• SDD_LOG_FORMAT - json/text (default: json)

Example structured log output:

{
  "timestamp": "2025-11-11T18:24:24.112289+00:00",
  "level": "INFO",
  "logger": "sdd-mcp",
  "message": "MCP server initialized successfully",
  "module": "__init__",
  "function": "create_app",
  "line": 95
}

• Linked relevant spec/task IDs (e.g., tasks/0002-spec-open-source-ready.md)
• Ran tests: uv run pytest
• Ran linters/hooks: uv run pre-commit run --all-files
• Updated docs or prompts if behavior changed

Warning

Firewall rules blocked me from connecting to one or more addresses (expand for details)

I tried to connect to the following addresses, but was blocked by firewall rules:

• astral.sh
  • Triggering command: curl -LsSf REDACTED (dns block)

If you need me to access, download, or install something from one of these locations, you can either:

• Configure Actions setup steps to set up my environment, which run before the firewall is enabled
• Add the appropriate URLs or hosts to the custom allowlist in this repository's Copilot coding agent settings (admins only)

Original prompt

Let's work on this issue @liatrio-labs/spec-driven-workflow/issues/5

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