fix: Address Gemini Code Assist review feedback

- Repository URL consistency: Updated all references to BeehiveInnovations/zen-mcp-server format
- Documentation clarity: Fixed misleading table headers and improved Docker configuration examples
- File conventions: Added missing final newlines to all files
- Configuration consistency: Clarified API key placeholder format in documentation

Addresses all points raised in PR #17 review by Gemini Code Assist.

🤖 Generated with Claude Code

Co-Authored-By: Claude <noreply@anthropic.com>

.claude/settings.example.json

@@ -33,3 +33,4 @@
     "gemini"
   ]
 }
+

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -12,7 +12,7 @@ body:
     attributes:
       label: Project Version
       description: "Which version are you using? (e.g., Docker image tag like `latest` or `v1.2.3`, or a git commit SHA)"
-      placeholder: "e.g., ghcr.io/beehiveinnovations/gemini-mcp-server:latest"
+      placeholder: "e.g., ghcr.io/beehiveinnovations/zen-mcp-server:latest"
     validations:
       required: true
 
@@ -78,3 +78,4 @@ body:
           required: true
         - label: I have confirmed that my `GEMINI_API_KEY` is set correctly.
           required: true
+

.github/ISSUE_TEMPLATE/config.yml

@@ -1,11 +1,12 @@
 blank_issues_enabled: false
 contact_links:
   - name: 💬 General Discussion
-    url: https://github.com/BeehiveInnovations/gemini-mcp-server/discussions
+    url: https://github.com/BeehiveInnovations/zen-mcp-server/discussions
     about: Ask questions, share ideas, or discuss usage patterns with the community
   - name: 📚 Documentation
-    url: https://github.com/BeehiveInnovations/gemini-mcp-server/blob/main/README.md
+    url: https://github.com/BeehiveInnovations/zen-mcp-server/blob/main/README.md
     about: Check the README for setup instructions and usage examples
   - name: 🤝 Contributing Guide
-    url: https://github.com/BeehiveInnovations/gemini-mcp-server/blob/main/CONTRIBUTING.md
+    url: https://github.com/BeehiveInnovations/zen-mcp-server/blob/main/CONTRIBUTING.md
     about: Learn how to contribute to the project
+

.github/ISSUE_TEMPLATE/documentation.yml

@@ -45,12 +45,12 @@ body:
       placeholder: |
         Change:
         ```
-        docker run ghcr.io/beehiveinnovations/gemini-mcp-server:latest
+        docker run ghcr.io/beehiveinnovations/zen-mcp-server:latest
         ```
         
         To:
         ```
-        docker run --pull=always ghcr.io/beehiveinnovations/gemini-mcp-server:latest
+        docker run --pull=always ghcr.io/beehiveinnovations/zen-mcp-server:latest
         ```
 
   - type: dropdown
@@ -65,3 +65,4 @@ body:
         - All users
     validations:
       required: true
+

.github/ISSUE_TEMPLATE/feature_request.yml

@@ -49,3 +49,4 @@ body:
       label: Contribution
       options:
         - label: I am willing to submit a Pull Request to implement this feature.
+

.github/ISSUE_TEMPLATE/tool_addition.yml

@@ -72,3 +72,4 @@ body:
       options:
         - label: I am willing to submit a Pull Request to implement this new tool.
         - label: I have checked that this tool doesn't overlap significantly with existing tools (analyze, codereview, debug, thinkdeep, chat).
+

.github/workflows/auto-version.yml

@@ -245,3 +245,4 @@ jobs:
           echo "- **PR**: #${{ github.event.pull_request.number }}" >> $GITHUB_STEP_SUMMARY
           echo "- **Title**: ${{ github.event.pull_request.title }}" >> $GITHUB_STEP_SUMMARY
         fi
+

.github/workflows/build_and_publish_docker.yml

@@ -8,7 +8,7 @@ on:
 
 env:
   REGISTRY: ghcr.io
-  IMAGE_NAME: patrykiti/zen-mcp-server
+  IMAGE_NAME: beehiveinnovations/zen-mcp-server
 
 jobs:
   build-and-push:
@@ -143,13 +143,13 @@ jobs:
         echo "Updating README.md with latest Docker image: $LATEST_TAG"
         
         # Update README.md with the latest image tag
-        sed -i.bak "s|ghcr\.io/patrykiti/zen-mcp-server:[a-zA-Z0-9\._-]*|$LATEST_TAG|g" README.md
+        sed -i.bak "s|ghcr\.io/[^/]*/zen-mcp-server:[a-zA-Z0-9\._-]*|$LATEST_TAG|g" README.md
         
         # Also update docs/user-guides/installation.md
-        sed -i.bak "s|ghcr\.io/patrykiti/zen-mcp-server:[a-zA-Z0-9\._-]*|$LATEST_TAG|g" docs/user-guides/installation.md
+        sed -i.bak "s|ghcr\.io/[^/]*/zen-mcp-server:[a-zA-Z0-9\._-]*|$LATEST_TAG|g" docs/user-guides/installation.md
         
         # Also update docs/user-guides/configuration.md  
-        sed -i.bak "s|ghcr\.io/patrykiti/zen-mcp-server:[a-zA-Z0-9\._-]*|$LATEST_TAG|g" docs/user-guides/configuration.md
+        sed -i.bak "s|ghcr\.io/[^/]*/zen-mcp-server:[a-zA-Z0-9\._-]*|$LATEST_TAG|g" docs/user-guides/configuration.md
         
         # Check if there are any changes
         if git diff --quiet README.md docs/user-guides/installation.md docs/user-guides/configuration.md; then
@@ -193,3 +193,4 @@ jobs:
           echo "### 📝 Documentation Updated" >> $GITHUB_STEP_SUMMARY
           echo "README.md and user guides have been automatically updated with the new Docker image tag: \`$LATEST_TAG\`" >> $GITHUB_STEP_SUMMARY
         fi
+

.github/workflows/docker-test.yml

@@ -29,3 +29,4 @@ jobs:
         echo "### ✅ Docker Build Test Passed" >> $GITHUB_STEP_SUMMARY
         echo "" >> $GITHUB_STEP_SUMMARY
         echo "Docker image builds successfully and is ready for production." >> $GITHUB_STEP_SUMMARY
+

.github/workflows/test.yml

@@ -115,3 +115,4 @@ jobs:
       run: |
         echo "🔒 Simulation tests skipped (no API keys configured)"
         echo "To enable simulation tests, add GEMINI_API_KEY and/or OPENAI_API_KEY as repository secrets"
+

CONTRIBUTING.md

@@ -1,4 +1,4 @@
-# Contributing to Gemini MCP Server
+# Contributing to Zen MCP Server
 
 Thank you for your interest in contributing! This guide explains how to set up the development environment and contribute to the project.
 
@@ -6,8 +6,8 @@ Thank you for your interest in contributing! This guide explains how to set up t
 
 1. **Clone the repository**
    ```bash
-   git clone https://github.com/BeehiveInnovations/gemini-mcp-server.git
-   cd gemini-mcp-server
+   git clone https://github.com/BeehiveInnovations/zen-mcp-server.git
+   cd zen-mcp-server
    ```
 
 2. **Create virtual environment**

README.md

@@ -200,7 +200,7 @@ have produced a configuration for you to copy:
 
 ```bash
 # Pull the latest published image
-docker pull ghcr.io/patrykiti/zen-mcp-server:v4.0.10
+docker pull ghcr.io/beehiveinnovations/zen-mcp-server:v4.0.10
 ```
 
 **Claude Desktop Configuration:**
@@ -212,7 +212,7 @@ docker pull ghcr.io/patrykiti/zen-mcp-server:v4.0.10
       "args": [
         "run", "--rm", "-i",
         "-e", "GEMINI_API_KEY",
-        "ghcr.io/patrykiti/zen-mcp-server:v4.0.10"
+        "ghcr.io/beehiveinnovations/zen-mcp-server:v4.0.10"
       ],
       "env": {
         "GEMINI_API_KEY": "your-gemini-api-key-here"
@@ -238,7 +238,7 @@ You can customize the server behavior by adding additional environment variables
         "-e", "DEFAULT_THINKING_MODE_THINKDEEP",
         "-e", "LOG_LEVEL",
         "-e", "MCP_PROJECT_ROOT",
-        "ghcr.io/patrykiti/zen-mcp-server:v4.0.10"
+        "ghcr.io/beehiveinnovations/zen-mcp-server:v4.0.10"
       ],
       "env": {
         "GEMINI_API_KEY": "your-gemini-api-key-here",
@@ -1095,7 +1095,7 @@ Once set up, everything works normally:
 
 ```bash
 # Pull the image (runs in WSL2 automatically)
-docker pull ghcr.io/patrykiti/zen-mcp-server:v4.0.10
+docker pull ghcr.io/beehiveinnovations/zen-mcp-server:v4.0.10
 
 # Configure Claude Desktop normally in Windows
 # Docker Desktop handles WSL2 routing automatically
@@ -1112,7 +1112,7 @@ If you prefer not to use Docker:
 
 ```powershell
 # In PowerShell or Command Prompt
-git clone https://github.com/PatrykIti/zen-mcp-server.git
+git clone https://github.com/BeehiveInnovations/zen-mcp-server.git
 cd zen-mcp-server
 pip install -r requirements.txt
 

claude_config_example.json

@@ -15,3 +15,4 @@
     }
   }
 }
+

docs/README.md

@@ -53,8 +53,8 @@ This documentation is organized into four main categories to serve different aud
 
 The server provides six specialized tools for different AI collaboration scenarios:
 
-| Tool | Purpose | Best For | Documentation |
-|------|---------|----------|---------------|
+| Tool | Purpose | Best For | Complexity Level |
+|------|---------|----------|------------------|
 | **[chat](api/tools/chat.md)** | Quick questions, brainstorming | Immediate answers, idea exploration | Low complexity, fast iteration |
 | **[thinkdeep](api/tools/thinkdeep.md)** | Complex analysis, strategic planning | Architecture decisions, system design | High complexity, deep analysis |
 | **[analyze](api/tools/analyze.md)** | Code exploration, system understanding | Codebase comprehension, dependency analysis | Medium complexity, systematic exploration |
@@ -159,3 +159,4 @@ To contribute:
 ---
 
 **Need Help?** Check the [Troubleshooting Guide](user-guides/troubleshooting.md) or explore the specific documentation section for your use case. For development questions, start with the [Contributing Guidelines](contributing/setup.md).
+

docs/api/tools/analyze.md

@@ -581,3 +581,4 @@ The authentication system uses JWT tokens with RSA256 signing:
 ---
 
 The Analyze Tool serves as your code comprehension partner, providing deep insights into existing systems and enabling informed decision-making for development and modernization efforts.
+

docs/api/tools/chat.md

@@ -351,3 +351,4 @@ The **Chat Tool** provides immediate access to Gemini's conversational capabilit
 ---
 
 The Chat Tool serves as the primary interface for rapid AI collaboration, providing immediate access to Gemini's knowledge while maintaining conversation context and enabling seamless integration with deeper analysis tools.
+

docs/api/tools/codereview.md

@@ -416,3 +416,4 @@ memory.create_entities([{
 ---
 
 The CodeReview Tool provides systematic, thorough code analysis that integrates seamlessly with development workflows while maintaining high standards for security, performance, and maintainability.
+

docs/api/tools/debug.md

@@ -406,3 +406,4 @@ Error Context:
 ---
 
 The Debug Tool provides systematic, expert-level debugging capabilities that can handle complex production issues while maintaining accuracy and providing actionable solutions for rapid incident resolution.
+

docs/api/tools/precommit.md

@@ -447,3 +447,4 @@ memory.create_entities([{
 ---
 
 The Precommit Tool provides comprehensive, automated quality assurance that integrates seamlessly with development workflows while maintaining high standards for security, performance, and code quality.
+

docs/api/tools/thinkdeep.md

@@ -474,3 +474,4 @@ Constraints:
 ---
 
 The ThinkDeep Tool serves as your strategic thinking partner, providing comprehensive analysis and creative problem-solving capabilities for the most challenging technical and architectural decisions.
+

docs/architecture/components.md

@@ -377,3 +377,4 @@ MAX_CONTEXT_TOKENS = int(os.getenv('MAX_CONTEXT_TOKENS', '1000000'))
 ---
 
 This component architecture provides a robust foundation for AI collaboration while maintaining security, performance, and extensibility requirements.
+

docs/architecture/data-flow.md

@@ -543,3 +543,4 @@ class PerformanceMetrics:
 ```
 
 This comprehensive data flow documentation provides the foundation for understanding how information moves through the Gemini MCP Server, enabling effective debugging, optimization, and extension of the system.
+

docs/architecture/overview.md

@@ -223,3 +223,4 @@ class ThreadContext:
 ---
 
 This architecture provides a robust, secure, and extensible foundation for AI-assisted development workflows while maintaining clear separation of concerns and comprehensive error handling.
+

docs/contributing/code-style.md

@@ -600,3 +600,4 @@ repos:
 ---
 
 Following these code style guidelines ensures consistent, maintainable, and secure code across the Gemini MCP Server project. All team members should adhere to these standards and use the automated tools to enforce compliance.
+

docs/contributing/file-overview.md

@@ -7,7 +7,7 @@ This document provides a comprehensive guide to the repository structure, explai
 ## Repository Structure
 
 ```
-gemini-mcp-server/
+zen-mcp-server/
 ├── CLAUDE.md                    # Collaboration framework and development guidelines
 ├── README.md                    # Project overview and quick start guide
 ├── LICENSE                      # Project license (MIT)
@@ -380,3 +380,4 @@ tests/
 ---
 
 This file overview provides the foundation for understanding the repository structure and serves as a guide for contributors to navigate the codebase effectively and make informed architectural decisions.
+

docs/contributing/setup.md

@@ -21,8 +21,8 @@ This guide helps you set up a development environment for contributing to the Ge
 ### 1. Clone Repository
 
 ```bash
-git clone https://github.com/BeehiveInnovations/gemini-mcp-server.git
-cd gemini-mcp-server
+git clone https://github.com/BeehiveInnovations/zen-mcp-server.git
+cd zen-mcp-server
 ```
 
 ### 2. Choose Development Method
@@ -378,3 +378,4 @@ docker system prune -f
 - Read [Development Workflows](workflows.md)
 - Review [Code Style Guide](code-style.md)
 - Understand [Testing Strategy](testing.md)
+

docs/contributing/test-structure.md

@@ -468,3 +468,4 @@ Clear organization and focused test files for easy maintenance
 ---
 
 This test structure demonstrates a mature, production-ready testing approach that ensures code quality, security, and reliability while supporting the collaborative AI development patterns that make this project unique.
+

docs/contributing/testing.md

@@ -688,3 +688,4 @@ For a comprehensive analysis of the existing test suite, including detailed brea
 ---
 
 This comprehensive testing strategy ensures high-quality, reliable code while maintaining development velocity and supporting the collaborative patterns defined in CLAUDE.md.
+

docs/contributing/workflows.md

@@ -573,8 +573,8 @@ claude-code-cli --tool precommit --path /workspace/
 **Docker Image Workflow**:
 ```bash
 # 1. Build and test image locally
-docker build -t gemini-mcp-server:latest .
-docker run --rm gemini-mcp-server:latest --version
+docker build -t zen-mcp-server:latest .
+docker run --rm zen-mcp-server:latest --version
 
 # 2. Push to registry (automated via GitHub Actions)
 # 3. Update deployment configurations
@@ -620,3 +620,4 @@ Implementation: Added context managers and explicit cleanup in utils/conversatio
 ---
 
 This development workflow ensures high-quality, collaborative development while maintaining consistency with CLAUDE.md patterns and preserving knowledge through the Memory Bank system.
+

docs/user-guides/configuration.md

@@ -8,7 +8,7 @@ This guide covers all configuration options for the Gemini MCP Server.
 
 | Variable | Description | Example |
 |----------|-------------|---------|
-| `GEMINI_API_KEY` | Your Gemini API key from Google AI Studio | `AIzaSyC...` |
+| `GEMINI_API_KEY` | Your Gemini API key from Google AI Studio (replace entire placeholder) | `AIzaSyC_your_actual_key_here` |
 
 ### Optional Configuration
 
@@ -43,10 +43,10 @@ Add to your Claude Desktop config file:
       "args": [
         "run", "--rm", "-i",
         "-e", "GEMINI_API_KEY",
-        "ghcr.io/patrykiti/gemini-mcp-server:latest"
+        "ghcr.io/beehiveinnovations/zen-mcp-server:latest"
       ],
       "env": {
-        "GEMINI_API_KEY": "your-gemini-api-key-here"
+        "GEMINI_API_KEY": "AIzaSyC_your_actual_gemini_api_key_here"
       }
     }
   }
@@ -75,10 +75,10 @@ Add to your Claude Desktop config file:
       "args": [
         "run", "--rm", "-i",
         "-e", "GEMINI_API_KEY",
-        "ghcr.io/patrykiti/gemini-mcp-server:v1.2.0"
+        "ghcr.io/beehiveinnovations/zen-mcp-server:v1.2.0"
       ],
       "env": {
-        "GEMINI_API_KEY": "your-gemini-api-key-here"
+        "GEMINI_API_KEY": "AIzaSyC_your_actual_gemini_api_key_here"
       }
     }
   }
@@ -289,3 +289,4 @@ services:
 **See Also:**
 - [Installation Guide](installation.md)
 - [Troubleshooting Guide](troubleshooting.md)
+

docs/user-guides/contributing-guide.md

@@ -108,13 +108,13 @@ After your PR is merged with a `+docker` prefix:
 
 ```bash
 # Pull your test image
-docker pull ghcr.io/patrykiti/gemini-mcp-server:pr-42
+docker pull ghcr.io/beehiveinnovations/zen-mcp-server:pr-42
 
 # Or use the commit-based tag
-docker pull ghcr.io/patrykiti/gemini-mcp-server:main-abc1234
+docker pull ghcr.io/beehiveinnovations/zen-mcp-server:main-abc1234
 
 # Test it locally
-docker run -it --rm ghcr.io/patrykiti/gemini-mcp-server:pr-42
+docker run -it --rm ghcr.io/beehiveinnovations/zen-mcp-server:pr-42
 ```
 
 ## Workflow Summary

docs/user-guides/installation.md

@@ -45,10 +45,10 @@ After following this guide, you'll have:
 
 ```bash
 # Download the latest stable version
-docker pull ghcr.io/patrykiti/gemini-mcp-server:latest
+docker pull ghcr.io/beehiveinnovations/zen-mcp-server:latest
 
 # Optional: Pull a specific version
-docker pull ghcr.io/patrykiti/gemini-mcp-server:v1.2.0
+docker pull ghcr.io/beehiveinnovations/zen-mcp-server:v1.2.0
 ```
 
 ### Step 2: Configure Claude Desktop
@@ -66,7 +66,7 @@ docker pull ghcr.io/patrykiti/gemini-mcp-server:v1.2.0
       "args": [
         "run", "--rm", "-i",
         "-e", "GEMINI_API_KEY",
-        "ghcr.io/patrykiti/gemini-mcp-server:latest"
+        "ghcr.io/beehiveinnovations/zen-mcp-server:latest"
       ],
       "env": {
         "GEMINI_API_KEY": "your-gemini-api-key-here"
@@ -86,10 +86,10 @@ Available image tags:
 
 ```bash
 # See all available tags
-docker search ghcr.io/patrykiti/gemini-mcp-server
+docker search ghcr.io/beehiveinnovations/zen-mcp-server
 
 # Or check GitHub Container Registry
-open https://github.com/PatrykIti/gemini-mcp-server/pkgs/container/gemini-mcp-server
+open https://github.com/BeehiveInnovations/zen-mcp-server/pkgs/container/zen-mcp-server
 ```
 
 ### Step 4: Test Installation
@@ -113,8 +113,8 @@ Restart Claude Desktop and try:
 ### Step 1: Clone Repository
 
 ```bash
-git clone https://github.com/BeehiveInnovations/gemini-mcp-server.git
-cd gemini-mcp-server
+git clone https://github.com/BeehiveInnovations/zen-mcp-server.git
+cd zen-mcp-server
 ```
 
 ### Step 2: One-Command Setup
@@ -198,7 +198,7 @@ services:
       - redis_data:/data
 
   gemini-mcp:
-    image: ghcr.io/beehiveinnovations/gemini-mcp-server:latest
+    image: ghcr.io/beehiveinnovations/zen-mcp-server:latest
     container_name: gemini-mcp-server
     restart: unless-stopped
     depends_on:
@@ -383,8 +383,8 @@ Once you're set up:
 
 1. **Explore the tools**: Try each tool to understand their specialties
 2. **Read the main README**: [Full documentation](../README.md) has advanced usage patterns
-3. **Join discussions**: [GitHub Discussions](https://github.com/BeehiveInnovations/gemini-mcp-server/discussions) for tips and tricks
-4. **Contribute**: Found a bug or want a feature? [Open an issue](https://github.com/BeehiveInnovations/gemini-mcp-server/issues)
+3. **Join discussions**: [GitHub Discussions](https://github.com/BeehiveInnovations/zen-mcp-server/discussions) for tips and tricks
+4. **Contribute**: Found a bug or want a feature? [Open an issue](https://github.com/BeehiveInnovations/zen-mcp-server/issues)
 
 ## 💡 Pro Tips
 
@@ -402,5 +402,5 @@ Once you're set up:
 
 **Need Help?** 
 - 📖 [Full Documentation](../README.md)
-- 💬 [Community Discussions](https://github.com/BeehiveInnovations/gemini-mcp-server/discussions)  
-- 🐛 [Report Issues](https://github.com/BeehiveInnovations/gemini-mcp-server/issues)
+- 💬 [Community Discussions](https://github.com/BeehiveInnovations/zen-mcp-server/discussions)  
+- 🐛 [Report Issues](https://github.com/BeehiveInnovations/zen-mcp-server/issues)

docs/user-guides/troubleshooting.md

@@ -393,8 +393,8 @@ cat .env | grep -v "GEMINI_API_KEY"
 ### Support Channels
 
 - 📖 [Documentation](../README.md)
-- 💬 [GitHub Discussions](https://github.com/BeehiveInnovations/gemini-mcp-server/discussions)
-- 🐛 [Issue Tracker](https://github.com/BeehiveInnovations/gemini-mcp-server/issues)
+- 💬 [GitHub Discussions](https://github.com/BeehiveInnovations/zen-mcp-server/discussions)
+- 🐛 [Issue Tracker](https://github.com/BeehiveInnovations/zen-mcp-server/issues)
 
 ### Creating Bug Reports