Add repo map, MCP baseline verification, and repo-specific agent skills

[Copilot]

Description

The issue requested a repo tree + mermaid diagram, a checklist covering agents/tools/MCP/PRs/deps/actions, live proof that MCP capability negotiation works for this repo, and 2+ skills tailored to the repo.

Repo map & checklist

• Added docs/REPO_MAP.md: top-level repo tree, Mermaid architecture diagram (host → MCP servers → tools/connectors/protocols), and an agentic-workflow checklist mapped to actual repo artifacts (agents/, mcp_server/main.py, .github/workflows/python-ci.yml, dependabot.yml, etc.)

MCP baseline verification

• Ran the existing JSON-RPC MCP server (mcp_server/main.py) live: initialize, tools/list, tools/call, and unknown-method error handling all behave correctly
• Added tests/test_mcp_baseline.py to pin down this baseline capability negotiation so it stays verified going forward

server = MCPServer()
await server.handle_request({"jsonrpc": "2.0", "id": 1, "method": "initialize",
    "params": {"clientInfo": {"name": "client", "version": "1.0"}}})
# -> serverInfo + capabilities.tools/resources

Repo-specific skills

• .github/skills/mcp-protocol-debugging/ — exercising/debugging the MCP JSON-RPC server
• .github/skills/quantum-connector-testing/ — testing the D-Wave quantum connector without a live QPU token, consistent with this repo's existing "no mocks/simulation in production" convention

No production code was modified; changes are additive (docs, skills, tests).

Type of change

• Bug fix
• New feature
• Breaking change
• Documentation update
• Other (describe):

Checklist

• My code follows the style guidelines of this project
• I have performed a self-review of my code
• I have commented my code, particularly in hard-to-understand areas
• I have made corresponding changes to the documentation
• My changes generate no new warnings
• I have added tests that prove my fix is effective or that my feature works
• New and existing unit tests pass locally with my changes
• Any dependent changes have been merged and published in downstream modules

Screenshots (if applicable)

Additional context

Pre-existing unrelated test failures (tests/test_pattern_detector.py missing psycopg2, tests/test_dependabot_test.py import issue) were observed but are out of scope for this change.

• Fixes REPO UPDATE-> follow steps prove verification on implementation by running it live. #125

[Copilot]

🟡 Changes recommended

A few newly added documentation/skill statements are objectively inaccurate or reference non-existent tooling and should be corrected to avoid misleading future contributors/agents.

Once you've addressed the issues Copilot identified, you can request another Copilot review.

Pull request overview

Adds repository-orientation documentation, repo-specific agent skills, and a new pytest baseline that pins down the current JSON-RPC MCP server handshake behavior for capability negotiation.

Changes:

• Added docs/REPO_MAP.md with a top-level repo map, Mermaid architecture diagram, and an agent-run checklist mapped to repo artifacts.
• Added tests/test_mcp_baseline.py to verify initialize, tools/list, tools/call, and unknown-method JSON-RPC error behavior for mcp_server/main.py.
• Added two repo-specific agent skills under .github/skills/ for MCP protocol debugging and quantum connector testing guidance.

File summaries

File	Description
tests/test_mcp_baseline.py	Adds baseline tests that exercise MCP JSON-RPC handshake and tool execution paths.
docs/REPO_MAP.md	Provides a repo map + checklist + MCP baseline documentation for agents and contributors.
.github/skills/quantum-connector-testing/SKILL.md	Adds guidance for testing D-Wave integration without introducing simulation/mocks in production paths.
.github/skills/mcp-protocol-debugging/SKILL.md	Adds a step-by-step guide for driving and debugging mcp_server/main.py MCP negotiation and tool calls.

Review details

• Files reviewed: 4/4 changed files
• Comments generated: 4
• Review effort level: Lite

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