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fix: rebranding, see [docs/name-change.md](docs/name-change.md) for details
🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <noreply@anthropic.com>
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.dockerignore

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env/
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venv/
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.venv/
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.zen_venv/
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.pal_venv/
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ENV/
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env.bak/
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venv.bak/

.env.example

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# Zen MCP Server Environment Configuration
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# PAL MCP Server Environment Configuration
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# Copy this file to .env and fill in your values
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# API Keys - At least one is required
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# LOCALE=fr-FR
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# ===========================================
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# Zen MCP Server Configuration
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# PAL MCP Server Configuration
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# ===========================================
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# Force .env file values to override system environment variables
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# Development with multiple AI tools: true (prevents tool conflicts)
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# Production/Container deployments: false (preserves security practices)
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# CI/CD environments: false (respects pipeline secrets)
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ZEN_MCP_FORCE_ENV_OVERRIDE=false
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PAL_MCP_FORCE_ENV_OVERRIDE=false
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# ===========================================
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# Docker Configuration
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# ===========================================
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# Container name for Docker Compose
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# Used when running with docker-compose.yml
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COMPOSE_PROJECT_NAME=zen-mcp
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COMPOSE_PROJECT_NAME=pal-mcp
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# Timezone for Docker containers
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# Ensures consistent time handling in containerized environments

.github/ISSUE_TEMPLATE/bug_report.yml

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attributes:
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label: Project Version
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description: "Which version are you using? (To see version: ./run-server.sh -v)"
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placeholder: "e.g., 5.1.0"
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placeholder: "e.g., 9.4.1"
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validations:
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required: true
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id: logs
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attributes:
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label: Relevant Log Output
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description: "Please copy and paste any relevant log output. Logs are stored under the `logs` folder in the zen folder. You an also use `./run-server.sh -f` to see logs"
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description: "Please copy and paste any relevant log output. Logs are stored under the `logs` folder in the pal folder. You an also use `./run-server.sh -f` to see logs"
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render: shell
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- type: dropdown

.github/ISSUE_TEMPLATE/config.yml

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blank_issues_enabled: false
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contact_links:
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- name: 💬 General Discussion
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url: https://github.com/BeehiveInnovations/zen-mcp-server/discussions
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url: https://github.com/BeehiveInnovations/pal-mcp-server/discussions
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about: Ask questions, share ideas, or discuss usage patterns with the community
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- name: 📚 Documentation
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url: https://github.com/BeehiveInnovations/zen-mcp-server/blob/main/README.md
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url: https://github.com/BeehiveInnovations/pal-mcp-server/blob/main/README.md
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about: Check the README for setup instructions and usage examples
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- name: 🤝 Contributing Guide
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url: https://github.com/BeehiveInnovations/zen-mcp-server/blob/main/CONTRIBUTING.md
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url: https://github.com/BeehiveInnovations/pal-mcp-server/blob/main/CONTRIBUTING.md
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about: Learn how to contribute to the project
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.github/ISSUE_TEMPLATE/tool_addition.yml

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name: 🛠️ New Gemini Tool Proposal
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description: Propose a new Zen MCP tool (e.g., `summarize`, `fixer`, `refactor`)
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description: Propose a new PAL MCP tool (e.g., `summarize`, `fixer`, `refactor`)
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labels: ["enhancement", "new-tool"]
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body:
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- type: input
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id: purpose
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attributes:
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label: What is the primary purpose of this tool?
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description: "Explain the tool's core function and the value it provides to developers using Claude + Zen."
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description: "Explain the tool's core function and the value it provides to developers using Claude + PAL."
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placeholder: "This tool will automatically generate comprehensive documentation from code, extracting class and function signatures, docstrings, and creating usage examples."
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validations:
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required: true
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description: "Show how a user would invoke this tool through Claude and what the expected output would look like."
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placeholder: |
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**User prompt to Claude:**
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"Use zen to generate documentation for my entire src/ directory"
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"Use pal to generate documentation for my entire src/ directory"
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**Expected behavior:**
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- Analyze all Python files in src/
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id: system-prompt
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label: Proposed System Prompt (Optional)
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description: "If you have ideas for how zen should be prompted for this tool, share them here."
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description: "If you have ideas for how pal should be prompted for this tool, share them here."
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placeholder: |
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You are an expert technical documentation generator. Your task is to create comprehensive, user-friendly documentation from source code...
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.github/workflows/docker-pr.yml

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```json
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{
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"mcpServers": {
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"zen": {
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"pal": {
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"command": "docker",
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"args": ["run", "--rm", "-i", "-e", "GEMINI_API_KEY", "ghcr.io/${{ github.repository }}:pr-${{ github.event.number }}"],
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"env": { "GEMINI_API_KEY": "your-key" }

.github/workflows/docker-release.yml

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\`\`\`json
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{
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"mcpServers": {
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"zen-mcp-server": {
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"pal-mcp-server": {
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"command": "docker",
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"run", "--rm", "-i",

.gitignore

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.claude/settings.local.json
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# Standalone mode files
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.zen_venv/
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.pal_venv/
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.docker_cleaned
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logs/
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*.backup

.pre-commit-config.yaml

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\.pal_venv/|
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AGENTS.md

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Also read CLAUDE.md and CLAUDE.local.md if available.
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## Project Structure & Module Organization
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Zen MCP Server centers on `server.py`, which exposes MCP entrypoints and coordinates multi-model workflows.
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PAL MCP Server centers on `server.py`, which exposes MCP entrypoints and coordinates multi-model workflows.
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Feature-specific tools live in `tools/`, provider integrations in `providers/`, and shared helpers in `utils/`.
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Prompt and system context assets stay in `systemprompts/`, while configuration templates and automation scripts live under `conf/`, `scripts/`, and `docker/`.
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Unit tests sit in `tests/`; simulator-driven scenarios and log utilities are in `simulator_tests/` with the `communication_simulator_test.py` harness.
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Authoritative documentation and samples live in `docs/`, and runtime diagnostics are rotated in `logs/`.
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## Build, Test, and Development Commands
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- `source .zen_venv/bin/activate` – activate the managed Python environment.
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- `source .pal_venv/bin/activate` – activate the managed Python environment.
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- `./run-server.sh` – install dependencies, refresh `.env`, and launch the MCP server locally.
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- `./code_quality_checks.sh` – run Ruff autofix, Black, isort, and the default pytest suite.
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- `python communication_simulator_test.py --quick` – smoke-test orchestration across tools and providers.
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- `./run_integration_tests.sh [--with-simulator]` – exercise provider-dependent flows against remote or Ollama models.
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Run code quality checks:
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```bash
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.zen_venv/bin/activate && ./code_quality_checks.sh
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.pal_venv/bin/activate && ./code_quality_checks.sh
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```
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For example, this is how we run an individual / all tests:
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```bash
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.zen_venv/bin/activate && pytest tests/test_auto_mode_model_listing.py -q
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.zen_venv/bin/activate && pytest -q
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.pal_venv/bin/activate && pytest tests/test_auto_mode_model_listing.py -q
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.pal_venv/bin/activate && pytest -q
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```
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## Coding Style & Naming Conventions

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