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+# Gemini MCP Server Documentation
+
+Welcome to the comprehensive documentation for the **Gemini MCP Server** - a sophisticated Model Context Protocol server that enables Claude to access Google's Gemini AI models through specialized tools for AI-assisted development workflows.
+
+## 📖 Documentation Overview
+
+This documentation is organized into four main categories to serve different audiences and use cases:
+
+### 🚀 For End Users
+- **[Installation Guide](user-guides/installation.md)** - Set up the server locally or with Docker
+- **[Configuration](user-guides/configuration.md)** - Configure the server for your environment  
+- **[Troubleshooting](user-guides/troubleshooting.md)** - Common issues and solutions
+
+### 🛠️ For Developers
+- **[Development Setup](contributing/setup.md)** - Set up your development environment
+- **[Development Workflows](contributing/workflows.md)** - Git workflows, testing, and collaboration patterns
+- **[Code Style Guide](contributing/code-style.md)** - Coding standards and best practices
+- **[Testing Strategy](contributing/testing.md)** - Testing approaches and quality assurance
+- **[Repository Overview](contributing/file-overview.md)** - Understanding the codebase structure
+
+### 🏗️ For System Architects
+- **[Architecture Overview](architecture/overview.md)** - High-level system design and components
+- **[Component Details](architecture/components.md)** - Detailed component descriptions and interactions
+- **[Data Flow Patterns](architecture/data-flow.md)** - How data moves through the system
+- **[Architecture Decisions](architecture/decisions/)** - Architecture Decision Records (ADRs)
+
+### 🔧 For API Users
+- **[MCP Protocol](api/mcp-protocol.md)** - Model Context Protocol implementation details
+- **[Tool Reference](api/tools/)** - Individual tool API documentation
+
+## 🎯 Quick Start Paths
+
+### New User Journey
+1. **[Install the Server](user-guides/installation.md)** → Get up and running quickly
+2. **[Configure Your Setup](user-guides/configuration.md)** → Customize for your environment
+3. **[Start Using Tools](#tool-reference)** → Explore AI-assisted workflows
+4. **[Troubleshoot Issues](user-guides/troubleshooting.md)** → Resolve common problems
+
+### Developer Journey  
+1. **[Set Up Development](contributing/setup.md)** → Prepare your dev environment
+2. **[Understand the Codebase](contributing/file-overview.md)** → Navigate the repository
+3. **[Follow Workflows](contributing/workflows.md)** → Git, testing, and collaboration
+4. **[Code Quality Standards](contributing/code-style.md)** → Maintain code quality
+
+### Architect Journey
+1. **[System Overview](architecture/overview.md)** → Understand the high-level design
+2. **[Component Architecture](architecture/components.md)** → Deep dive into system parts
+3. **[Data Flow Analysis](architecture/data-flow.md)** → Trace information flow
+4. **[Decision Context](architecture/decisions/)** → Understand design choices
+
+## 🛠️ Tool Reference
+
+The server provides six specialized tools for different AI collaboration scenarios:
+
+| Tool | Purpose | Best For | Documentation |
+|------|---------|----------|---------------|
+| **[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 |
+| **[codereview](api/tools/codereview.md)** | Code quality, security, bug detection | PR reviews, security audits | Quality assurance, comprehensive validation |
+| **[debug](api/tools/debug.md)** | Root cause analysis, error investigation | Bug fixing, performance issues | Problem-solving, systematic debugging |
+| **[precommit](api/tools/precommit.md)** | Automated quality gates | Pre-commit validation, change analysis | Quality gates, automated validation |
+
+### Tool Selection Guide
+
+**For Quick Tasks**: Start with [chat](api/tools/chat.md) for immediate answers and brainstorming
+**For Complex Planning**: Use [thinkdeep](api/tools/thinkdeep.md) for architecture and strategic decisions  
+**For Code Understanding**: Use [analyze](api/tools/analyze.md) to explore and understand existing code
+**For Quality Assurance**: Use [codereview](api/tools/codereview.md) and [precommit](api/tools/precommit.md) for validation
+**For Problem Solving**: Use [debug](api/tools/debug.md) for systematic error investigation
+
+## 🔄 Collaboration Framework
+
+This project follows the **[CLAUDE.md Collaboration Framework](../CLAUDE.md)** which defines:
+- **Tool Selection Matrix**: Guidelines for choosing the right tool for each task
+- **Memory Bank Integration**: Context preservation across development sessions  
+- **Quality Gates**: Mandatory validation and review processes
+- **Documentation Standards**: Comprehensive documentation requirements
+
+### Key Collaboration Patterns
+- **Complex Tasks (>3 steps)**: Always use TodoWrite to plan and track progress
+- **Architecture Decisions**: Must involve `thinkdeep` for exploration before implementation
+- **Code Reviews**: All significant changes require `codereview` analysis before committing
+- **Documentation Updates**: Any code change must include corresponding documentation updates
+
+## 📚 Additional Resources
+
+### Configuration Examples
+- **[macOS Setup](../examples/claude_config_macos.json)** - Local development on macOS
+- **[WSL Setup](../examples/claude_config_wsl.json)** - Windows Subsystem for Linux
+- **[Docker Setup](../examples/claude_config_docker_home.json)** - Container-based deployment
+
+### Project Information
+- **[Main README](../README.md)** - Project overview and quick start
+- **[Contributing Guidelines](../CONTRIBUTING.md)** - How to contribute to the project
+- **[License](../LICENSE)** - MIT License details
+- **[Collaboration Framework](../CLAUDE.md)** - Development collaboration patterns
+
+### Memory Bank System
+The project uses a **Memory Bank** system for context preservation:
+- **[Product Context](../memory-bank/productContext.md)** - Project goals and architecture
+- **[Active Context](../memory-bank/activeContext.md)** - Current development status
+- **[Decision Log](../memory-bank/decisionLog.md)** - Architectural decisions and rationale
+- **[Progress Tracking](../memory-bank/progress.md)** - Task completion and milestones
+
+## 🎨 Documentation Standards
+
+### For Technical Audiences
+- **Code Context**: All explanations include specific file and line number references (`file_path:line_number`)
+- **Architecture Focus**: Explain *why* decisions were made, not just *what* was implemented
+- **Data Flow**: Trace data through the system with concrete examples
+- **Error Scenarios**: Document failure modes and recovery strategies
+
+### For Non-Technical Audiences  
+- **Plain Language**: Avoid jargon, explain technical terms when necessary
+- **Purpose-Driven**: Start with "what problem does this solve?"
+- **Visual Aids**: Use diagrams and flowcharts where helpful
+- **Practical Examples**: Show real usage scenarios
+
+## 🔍 Finding What You Need
+
+### By Role
+- **System Administrators**: Start with [Installation](user-guides/installation.md) and [Configuration](user-guides/configuration.md)
+- **End Users**: Begin with [Tool Reference](#tool-reference) and [Quick Start](#new-user-journey)
+- **Developers**: Follow the [Developer Journey](#developer-journey) starting with [Development Setup](contributing/setup.md)
+- **Architects**: Review [Architecture Overview](architecture/overview.md) and [System Design](architecture/components.md)
+
+### By Task
+- **Setting Up**: [Installation](user-guides/installation.md) → [Configuration](user-guides/configuration.md)
+- **Using Tools**: [Tool Reference](#tool-reference) → Specific tool documentation
+- **Developing**: [Setup](contributing/setup.md) → [Workflows](contributing/workflows.md) → [Code Style](contributing/code-style.md)
+- **Understanding Architecture**: [Overview](architecture/overview.md) → [Components](architecture/components.md) → [Data Flow](architecture/data-flow.md)
+- **Troubleshooting**: [Troubleshooting Guide](user-guides/troubleshooting.md) or relevant tool documentation
+
+### By Problem Type
+- **Installation Issues**: [Installation Guide](user-guides/installation.md) and [Troubleshooting](user-guides/troubleshooting.md)
+- **Configuration Problems**: [Configuration Guide](user-guides/configuration.md)
+- **Tool Behavior Questions**: Specific [Tool Documentation](api/tools/)
+- **Development Questions**: [Contributing Guides](contributing/)
+- **Architecture Questions**: [Architecture Documentation](architecture/)
+
+## 📝 Contributing to Documentation
+
+This documentation follows the standards defined in [CLAUDE.md](../CLAUDE.md):
+
+1. **Accuracy**: Documentation must reflect actual code behavior
+2. **Completeness**: Cover all user-facing functionality  
+3. **Accessibility**: Understandable by intended audience
+4. **Currency**: Updated with every related code change
+
+To contribute:
+1. Follow the [Development Workflows](contributing/workflows.md)
+2. Maintain [Code Style Standards](contributing/code-style.md)
+3. Include comprehensive [Testing](contributing/testing.md)
+4. Update relevant documentation sections
+
+---
+
+**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).
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diff --git a/memory-bank/progress.md b/memory-bank/progress.md
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+++ b/memory-bank/progress.md
@@ -32,6 +32,7 @@ This file tracks the project's progress using a task list format.
 - ✅ docs/contributing/ completed (workflows.md, code-style.md, testing.md, file-overview.md)
 - ✅ Fixed all broken internal links in documentation per analysis
 - ✅ Complete documentation structure per CLAUDE.md standards implemented
+- ✅ docs/README.md created as central documentation hub with comprehensive navigation
 
 ## Next Steps