Added new confidence values (very_high, almost_certain) to all workflow tools
to provide more granular confidence tracking. Updated enum declarations in:
- analyze.py, codereview.py, debug.py, precommit.py, secaudit.py, testgen.py
- Updated debug.py's get_required_actions to handle new confidence values
- All tools now use consistent 7-value confidence scale
- refactor.py kept its unique scale (exploring/incomplete/partial/complete)
Also fixed model thinking configuration:
- Added very_high and almost_certain to MODEL_THINKING_PREFERENCES
- Set medium thinking for very_high, high thinking for almost_certain
- Updated prompts to clarify certain means 100% local confidence
🤖 Generated with [Claude Code](https://claude.ai/code)
Co-Authored-By: Claude <noreply@anthropic.com>
- Implemented `run-server.ps1` for setting up the Zen MCP server environment, including virtual environment creation, dependency installation, and Docker cleanup.
- Added logging and error handling throughout the setup process.
- Included functions for validating API keys and configuring integration with Claude Desktop and Gemini CLI.
- Created `run_integration_tests.ps1` to execute integration tests with real API calls, including checks for API key availability and environment setup.
- Enhanced output with color-coded messages for better user experience.
Patch directory added for cross-platform patching support (`patch_crossplatform.py`).
- Created build.sh script for building the Docker image with environment variable checks.
- Added deploy.sh script for deploying the Zen MCP Server with health checks and logging.
- Implemented healthcheck.py to verify server process, Python imports, log directory, and environment variables.
- Developed comprehensive tests for Docker configuration, environment validation, and integration with MCP.
- Included performance tests for Docker image size and startup time.
- Added validation script tests to ensure proper Docker and MCP setup.
* feat: Enhance run-server.sh with uv-first Python environment setup
- Implement uv-first approach for faster environment setup when available
- Add automatic WSL environment detection using wslvar for better Windows integration
- Improve system package installation by using bash -c for better command execution
- Add comprehensive environment validation and fallback mechanisms
- Optimize dependency installation with uv when environment supports it
- Enhance configuration display workflow for better user experience
- Add environment markers to track uv-created environments
- Improve error handling and user messaging throughout setup process
🤖 Generated with [Claude Code](https://claude.ai/code)
Co-Authored-By: Claude <noreply@anthropic.com>
* feat: Add .claude/settings.local.json to .gitignore
Personal Claude Code settings should not be tracked in source control.
Reference: https://docs.anthropic.com/en/docs/claude-code/settings🤖 Generated with [Claude Code](https://claude.ai/code)
Co-Authored-By: Claude <noreply@anthropic.com>
* feat: Add shared Claude Code settings.json for team defaults
- Add .claude/settings.json with default permissions for team use
- Remove .claude/settings.local.json from git tracking (now personal config)
Reference: https://docs.anthropic.com/en/docs/claude-code/settings🤖 Generated with [Claude Code](https://claude.ai/code)
Co-Authored-By: Claude <noreply@anthropic.com>
* fix: Address Gemini Code Assist review issues in run-server.sh
- Fix hardcoded Unix paths (lines 563 & 568) with cross-platform detection
- Improve error handling by capturing uv stderr instead of /dev/null
- Fix uv environment detection logic to check uv_created marker file
Resolves three issues identified in PR review:
1. High Priority: Replace hardcoded $VENV_PATH/bin/python with detection
2. Medium Priority: Capture and display uv command errors for debugging
3. Medium Priority: Use marker file instead of path matching for uv detection
🤖 Generated with [Claude Code](https://claude.ai/code)
Co-Authored-By: Claude <noreply@anthropic.com>
* fix: Address additional Gemini Code Assist feedback
- Enhance WSL warning message with more helpful guidance
- Add security comment explaining bash -c usage over eval
- Add get_venv_python_path helper function for cleaner cross-platform detection
- Improve path resolution error handling with proper error checking
Addresses 4 additional review points from gemini-code-assist to improve
user experience, code clarity, and error handling robustness.
🤖 Generated with [Claude Code](https://claude.ai/code)
Co-Authored-By: Claude <noreply@anthropic.com>
---------
Co-authored-by: Claude <noreply@anthropic.com>
## Description
This PR adds support for selectively disabling tools via the DISABLED_TOOLS environment variable, allowing users to customize which MCP tools are available in their Zen server instance. This feature enables better control over tool availability for security, performance, or organizational requirements.
## Changes Made
- [x] Added `DISABLED_TOOLS` environment variable support to selectively disable tools
- [x] Implemented tool filtering logic with protection for essential tools (version, listmodels)
- [x] Added comprehensive validation with warnings for unknown tools and attempts to disable essential tools
- [x] Updated `.env.example` with DISABLED_TOOLS documentation and examples
- [x] Added comprehensive test suite (16 tests) covering all edge cases
- [x] No breaking changes - feature is opt-in with default behavior unchanged
## Configuration
Add to `.env` file:
```bash
# Optional: Tool Selection
# Comma-separated list of tools to disable. If not set, all tools are enabled.
# Essential tools (version, listmodels) cannot be disabled.
# Available tools: chat, thinkdeep, planner, consensus, codereview, precommit,
# debug, docgen, analyze, refactor, tracer, testgen
# Examples:
# DISABLED_TOOLS= # All tools enabled (default)
# DISABLED_TOOLS=debug,tracer # Disable debug and tracer tools
# DISABLED_TOOLS=planner,consensus # Disable planning tools
