Add repo-specific repo assist map, MCP baseline verification, and project skills

.github/dependabot.yml

@@ -1,29 +1,14 @@
-groupthinking-patch-3
- # To get started with Dependabot version updates, you'll need to specify which
- master
-# package ecosystems to update and where the package manifests are located.
-# Please see the documentation for all configuration options:
-# https://docs.github.com/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file
-
 version: 2
 updates:
-groupthinking-patch-3
-  - package-ecosystem: "" # See documentation for possible values
-
- groupthinking-patch-2
-  - package-ecosystem: "" # See documentation for possible values
-
   - package-ecosystem: "pip"
-    directory: "/" # Location of package manifests
+    directory: "/"
     schedule:
       interval: "weekly"
   - package-ecosystem: "npm"
-    directory: "/frontend" # Location of package manifests
+    directory: "/frontend"
     schedule:
       interval: "weekly"
   - package-ecosystem: "docker"
-master
-master
-    directory: "/" # Location of package manifests
+    directory: "/"
     schedule:
       interval: "weekly"

.github/skills/codebase-summary/SKILL.md

@@ -0,0 +1,39 @@
+---
+name: codebase-summary
+description: Generate a repo-specific map of self-correcting-executor, including the tree, key dependencies, and MCP verification steps. Use this when asked to summarize the architecture or prepare an agent run for this repository.
+---
+
+When asked to summarize or orient an agent in this repository, use the current
+repo structure instead of generic MCP examples.
+
+1. Start from the current repository root (`git rev-parse --show-toplevel`).
+2. Build the summary around these directories:
+   - `agents/`
+   - `connectors/`
+   - `mcp_server/`
+   - `protocols/`
+   - `frontend/`
+   - `tests/`
+3. Call out the primary dependency sources:
+   - `requirements.txt`
+   - `requirements-ci.txt`
+   - `requirements-test.txt`
+   - `frontend/package.json`
+4. When MCP is relevant, explicitly distinguish:
+   - **host**: external Copilot/CLI/operator
+   - **client**: external MCP-aware caller
+   - **server**: the repo's implementations in `mcp_server/` and
+     `quantum_mcp_server/`
+5. Use the in-process handler checks before reporting that baseline as verified:
+
+   ```bash
+   cd "$(git rev-parse --show-toplevel)"
+   python -m scripts.verify_mcp_baseline
+   python -m pytest tests/test_mcp_baseline_verifier.py -q
+   ```
+
+   These checks exercise the custom handler in-process; they do not verify
+   an external MCP client/transport connection.
+
+6. Point the reader to `docs/REPO_MAP.md` for the maintained tree, mermaid
+   diagram, dependency snapshot, workflow checklist, and CI/MCP notes.

.github/skills/github-actions-failure-debugging/SKILL.md

@@ -0,0 +1,43 @@
+---
+name: github-actions-failure-debugging
+description: Guide for debugging failing GitHub Actions workflows in self-correcting-executor. Use this when asked to investigate Python CI, Frontend CI, or PR workflow failures in this repository.
+---
+
+Use GitHub MCP tools first, then reproduce locally with the repo's existing
+commands.
+
+1. List recent workflow runs for `groupthinking/self-correcting-executor`.
+   Focus on:
+   - `.github/workflows/python-ci.yml`
+   - `.github/workflows/frontend-ci.yml`
+2. Get job logs for the failed run or failed jobs.
+3. Interpret the result against this repo's workflow behavior:
+   - `python-ci.yml` runs `black --check .`
+   - `python-ci.yml` runs pytest as a blocking step. Its existing `flake8`
+     step remains advisory via `|| echo ...` and `continue-on-error`, so a
+     green workflow does not establish a lint-clean repository.
+   - `frontend-ci.yml` runs `npm ci || npm install`, then lint/test/build from
+     `/frontend`
+4. Reproduce only the relevant local command:
+
+   ```bash
+   cd "$(git rev-parse --show-toplevel)"
+   python -m pytest tests/ -q
+   cd "$(git rev-parse --show-toplevel)/frontend"
+   npm run lint
+   npm run build
+   ```
+
+5. If the failure touches MCP behavior, also run the repo's in-process MCP handler checks:
+
+   ```bash
+   cd "$(git rev-parse --show-toplevel)"
+   python -m scripts.verify_mcp_baseline
+   python -m pytest tests/test_mcp_baseline_verifier.py -q
+   ```
+
+   These checks exercise the custom handler in-process; they do not verify
+   an external MCP client/transport connection.
+
+6. Keep fixes surgical. Do not "clean up" unrelated files just because the
+   workflow surfaced pre-existing noise.

.github/workflows/python-ci.yml

@@ -31,8 +31,7 @@ jobs:
         run: flake8 . || echo "Flake8 found issues but continuing CI"
         continue-on-error: true
       - name: Run tests with coverage
-        run: pytest --cov=. || echo "Tests failed but continuing CI"
-        continue-on-error: true
+        run: pytest --cov=.
 
   actions:
     runs-on: ubuntu-latest

README.md

@@ -29,4 +29,10 @@ Open http://localhost:8080/health to verify the API is running.
 
 ## Development
 
-The workspace includes a **DevContainer** definition – simply open the folder in VS Code or Cursor and choose *Reopen in Container* to get an IDE connected to the running services. 
+The workspace includes a **DevContainer** definition – simply open the folder in VS Code or Cursor and choose *Reopen in Container* to get an IDE connected to the running services. 
+
+## Repo assist
+
+For a repo-specific map of the current tree, dependency snapshot, mermaid
+architecture diagram, MCP capability-verification notes, and agent workflow
+checklist, see [`docs/REPO_MAP.md`](docs/REPO_MAP.md).

docs/REPO_MAP.md

@@ -0,0 +1,185 @@
+# Repo Map, MCP Verification, and Agent Workflow Checklist
+
+This repository mixes agent orchestration, MCP servers, connectors, protocols,
+and a small frontend. This document makes the issue's requested "repo assist"
+material specific to `groupthinking/self-correcting-executor` so an agent can
+map the repo, verify the MCP handler in-process, and decide what to check before
+commit/merge.
+
+## Repo tree (focused map)
+
+```text
+self-correcting-executor/
+├── agents/                  # A2A framework, executor, mutator, MCP integrations
+│   ├── a2a_framework.py
+│   ├── a2a_mcp_integration.py
+│   ├── executor.py
+│   ├── mutator.py
+│   ├── specialized/
+│   └── unified/
+├── analyzers/               # Pattern analysis helpers
+├── auth/                    # Auth helpers
+├── config/                  # MCP and component configuration
+├── connectors/              # D-Wave, GitHub, LLM, xAI, MCP base connectors
+├── docs/                    # Architecture, planning, and task guides
+├── fabric/                  # State continuity and integrated MCP fabric
+├── frontend/                # Vite + React UI
+├── llm/                     # Continuous learning system
+├── mcp_runtime_template_hg/ # SDK/API/CLI MCP runtime template
+├── mcp_server/              # JSON-RPC MCP server + FastMCP-backed server
+├── middleware/              # Security middleware
+├── protocols/               # Executable protocols/tasks
+├── quantum_mcp_server/      # Quantum-focused MCP server variant
+├── scripts/                 # Setup, compliance, cleanup, security scripts
+├── test_data/               # Real input fixtures used by tests/scripts
+├── tests/                   # Pytest suite
+├── ui/                      # Additional UI assets and guide content
+└── utils/                   # Shared logging and DB tracking
+```
+
+## Dependency snapshot
+
+- Python runtime dependencies: `requirements.txt` currently pins **117**
+  packages, including `mcp`, `mcp-use`, FastAPI, D-Wave Ocean SDK, LangChain,
+  SQLAlchemy, Redis, and transformer-related packages.
+- CI/test dependencies: `requirements-ci.txt` contains the lightweight
+  verification stack (`black`, `flake8`, `pytest`, `pytest-cov`,
+  `pytest-asyncio`) plus the MCP, NumPy, and PostgreSQL imports needed by
+  the collected tests. MCP/Pydantic match the production compatibility pair.
+- Frontend runtime dependencies: `frontend/package.json` currently declares
+  **7** runtime packages (`react`, `react-dom`, `@tanstack/react-query`,
+  `axios`, `framer-motion`, `lucide-react`, `three`) and **12** dev
+  dependencies for TypeScript, ESLint, and Vite.
+
+## Mermaid diagram
+
+```mermaid
+flowchart TD
+    H[Host / Copilot / operator]
+    O[orchestrator.py<br/>orchestrator_mapreduce.py]
+
+    subgraph Servers[MCP servers]
+        M1[mcp_server/main.py<br/>custom JSON-RPC MCPServer]
+        M2[mcp_server/real_mcp_server.py<br/>FastMCP tool server]
+        M3[quantum_mcp_server/]
+    end
+
+    subgraph Tools[Declared MCP tools]
+        T1[code_analyzer]
+        T2[protocol_validator]
+        T3[self_corrector]
+    end
+
+    subgraph Connectors[Connectors]
+        C1[github_mcp_connector.py]
+        C2[dwave_quantum_connector.py]
+        C3[llm_connector.py]
+        C4[xai_connector.py]
+    end
+
+    subgraph Tasks[protocols/*.py]
+        P1[data_processor]
+        P2[file_validator]
+        P3[database_health_check]
+        P4[system_monitor]
+    end
+
+    H --> O
+    M1 --> T1
+    M1 --> T2
+    M1 --> T3
+    M2 --> C2
+    M2 --> P1
+    O --> Tasks
+    Tasks --> P1
+    Tasks --> P2
+    Tasks --> P3
+    Tasks --> P4
+```
+
+The MCP servers are separate entrypoints; no direct orchestrator-to-server
+call is implied. `real_mcp_server.py` imports the D-Wave connector and the
+data processor. Other connectors are shown as repository components, not
+as dependencies of that server.
+
+## Agentic workflow checklist for this repo
+
+- [x] **Agents**: `agents/a2a_framework.py`, `agents/a2a_mcp_integration.py`,
+      and `agents/unified/` contain agent coordination logic.
+- [x] **Tools**: `mcp_server/main.py` declares `code_analyzer`,
+      `protocol_validator`, and `self_corrector`.
+- [x] **MCP**: the repo is actively using MCP packages and MCP-shaped servers
+      (`mcp_server/main.py`, `mcp_server/real_mcp_server.py`,
+      `config/mcp_config.py`, `connectors/mcp_base.py`).
+- [x] **Pull / push / request / commit / merge**: human workflows use GitHub
+      pull requests; cloud-agent workflows in this repo should publish progress
+      via PR updates instead of pushing directly from the sandbox.
+- [x] **Issues**: link changes back to GitHub issues with `Closes #<number>`.
+- [x] **Code**: the main test entrypoint is `pytest` with `pytest.ini`
+      configured to use `tests/`.
+- [x] **Deps**: Python dependencies live in `requirements*.txt`; frontend
+      dependencies live in `frontend/package.json`.
+- [x] **Database**: DB-aware execution paths are visible in `utils/db_tracker.py`
+      and `protocols/database_health_check.py`.
+- [x] **Actions**: `.github/workflows/python-ci.yml` and
+      `.github/workflows/frontend-ci.yml` define CI.
+- [x] **Role assignment / security**: `auth/` and `middleware/` contain auth
+      and security logic.
+
+## MCP baseline: is this repo using MCP?
+
+Yes. The repository is using MCP in two forms:
+
+1. A custom JSON-RPC server in `mcp_server/main.py`
+   with explicit MCP methods such as `initialize`, `tools/list`, `tools/call`,
+   `resources/list`, and `resources/read`.
+2. A FastMCP-based server in `mcp_server/real_mcp_server.py`
+   built on the `mcp` package.
+
+The custom handler advertises protocol version `2024-11-05`. Direct calls
+can verify its advertised tool and resource behavior, but do not establish
+MCP specification compliance or successful transport negotiation with an
+external host/client. Those require a separate integration test.
+
+### Host / client / server mapping for this repo
+
+- **Host**: external agent host (for example Copilot, CLI, or another MCP-aware
+  operator) orchestrates requests and permissions.
+- **Client**: the MCP-aware caller is external to this repo; this repo does not
+  ship a standalone client implementation.
+- **Server**: this repo implements the server side in `mcp_server/` and
+  `quantum_mcp_server/`.
+
+## Live verification steps
+
+The focused verifier calls the custom handler in-process. It asserts the
+initialize response, the advertised/listed tool names, and the actual
+`code_analyzer` result. Any JSON-RPC error, missing capability or incorrect
+analysis raises an exception and makes the command exit unsuccessfully.
+This proves the handler behavior, not an external MCP transport connection.
+
+From any directory inside the checkout:
+
+```bash
+cd "$(git rev-parse --show-toplevel)"
+python -m scripts.verify_mcp_baseline
+python -m pytest tests/test_repo_assist_docs.py tests/test_mcp_baseline_verifier.py -q
+```
+
+## CI baseline observed from GitHub Actions
+
+- The repo has active `Python CI` and `Frontend CI` workflows.
+- `Python CI` runs `black --check .` as a blocking step. Inspect the current
+  head's logs; a previous run's result is not evidence for a new commit.
+- `pytest --cov=.` is blocking: collection failures and failed assertions fail
+  the matrix job. `flake8` remains advisory in the existing workflow, so a
+  green workflow alone does not prove the repository is free of lint findings.
+
+## Skills added for this repo
+
+Project-scoped skills now live under `.github/skills/`:
+
+- `github-actions-failure-debugging`: tailored to the repo's Python/Frontend CI
+  workflows and GitHub MCP debugging flow.
+- `codebase-summary`: tailored to this repo's tree mapping, dependency checks,
+  and MCP verification workflow.