[Copilot]

Summary

Adds a repository map, an architecture diagram tied to actual imports, an agent-workflow checklist, and two repository-specific skills: mcp-protocol-debugging and quantum-connector-testing. The repository map now shows the actual D-Wave/DataProcessor imports, uses actionable repository commands, and accurately distinguishes placeholder reporting from enforced assertions. The debugging and quantum-testing skills describe their actual checks.

The MCP checks exercise the existing custom JSON-RPC handler in-process. They verify the documented initialization, tool discovery/execution and error behavior; they do not establish external transport compatibility or complete MCP specification compliance.

Code and CI repairs

• Correct malformed Dependabot configuration for the actual pip, frontend npm and Docker manifests.
• Replace tests of a nonexistent Dependabot helper with assertions against the real configuration, manifests and workflow.
• Align CI's MCP/Pydantic dependencies and supply the imports needed by the existing tests. Exercise real FastMCP tool dispatch and temporary data fixtures.
• Keep pytest failures blocking and set pythonpath = . so the exact console command used by GitHub collects the repository packages.
• Apply the existing Black formatter without changing those formatted modules' behavior.

Validation

Current tested head: 258f1bfa4a85c5b0694b37a2902e11a24815f2b2.

• pytest --cov=.: 27 passed and 3 explicit integration skips on both Python 3.10 and 3.11, with PYTHONPATH and DWAVE_API_TOKEN unset.
• black --check .: passed on both versions.
• Current GitHub checks: 7 successful, 1 skipped (CodeRabbit), including both Python jobs, Actions validation and CodeQL.

The three integration skips require quantum configuration, a D-Wave token or an external local MCP service. No live QPU, provider or external MCP transport success is claimed. The existing flake8 step remains advisory, and a pre-existing coverage-parser warning limits coverage completeness; the passing jobs do not establish a lint-clean repository or complete coverage.

This addresses #125. PRs #126 and #127 are parallel proposals for that issue; this review does not choose or merge both alternatives.

[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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[groupthinking]

Reviewed the repaired current head 258f1bfa4a85c5b0694b37a2902e11a24815f2b2. The 4 remaining inline findings are addressed in the code and repository guidance. The exact CI pytest command passes with 27 tests and 3 explicit integration skips on both Python versions; all current hosted jobs have finished with 7 successes and only CodeRabbit skipped. The previously masked pytest failure is now blocking.

Approval covers this repository-guidance and CI change. MCP verification is in-process only; live QPU/provider/transport behavior is untested. Existing advisory flake8 and incomplete coverage are disclosed in the updated description. #126 and #127 are competing proposals for #125, so this approval does not authorize merging both or merging either automatically.

[groupthinking]

Closing as a duplicate of #127, which is now merged. Both PRs carried identical changes to dependabot.yml, python-ci.yml, orchestrator_mapreduce.py, pytest.ini, requirements-ci.txt and the Dependabot/MCP tests; #127 also adds the MCP baseline verifier script and docs tests. The only unique content here is the two skills (mcp-protocol-debugging, quantum-connector-testing) and a different REPO_MAP.md, which would conflict with #127's version. If those two skills are wanted, they can be cherry-picked into a small follow-up PR.