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+# MCP Documentation Index
+
+**Complete Index of Model Context Protocol Documentation**
+
+This index provides a comprehensive overview of all MCP documentation with summaries and quick links.
+
+---
+
+## 📚 Quick Navigation
+
+- [Getting Started](#getting-started)
+- [Core Documentation](#core-documentation)
+- [Hook System](#hook-system)
+- [Extension System](#extension-system)
+- [MCP Servers](#mcp-servers)
+- [API Reference](#api-reference)
+- [Development Documentation](#development-documentation)
+
+---
+
+## Getting Started
+
+### [Main README](3%20projects/OLLM%20CLI/MCP/README.md)
+
+**Overview and Navigation Guide**
+
+The main entry point for MCP documentation. Provides:
+
+- Complete documentation overview
+- Quick links for users, developers, and administrators
+- What is MCP explanation
+- Learning paths (beginner, intermediate, advanced)
+- Key concepts and common use cases
+- Troubleshooting guide
+- Status and roadmap
+
+**Topics:** Overview, Navigation, Learning Paths, Key Concepts  
+**Audience:** All users  
+**Length:** 500+ lines
+
+---
+
+### [Getting Started Guide](3%20projects/OLLM%20CLI/MCP/getting-started.md)
+
+**Quick Start Guide for MCP, Hooks, and Extensions**
+
+Step-by-step guide to get started with MCP features:
+
+- What is MCP and its three main features
+- Prerequisites and installation verification
+- Quick start examples
+- Using MCP servers (listing, starting, stopping)
+- Using hooks (creating, managing, trust levels)
+- Using extensions (searching, installing, managing)
+- Common workflows and troubleshooting
+
+**Topics:** Quick Start, MCP Servers, Hooks, Extensions, Examples  
+**Audience:** New users  
+**Length:** 600+ lines
+
+**Key Sections:**
+
+- [What is MCP?](3%20projects/OLLM%20CLI/MCP/getting-started.md#what-is-mcp)
+- [Using MCP Servers](3%20projects/OLLM%20CLI/MCP/getting-started.md#using-mcp-servers)
+- [Using Hooks](3%20projects/OLLM%20CLI/MCP/getting-started.md#using-hooks)
+- [Using Extensions](3%20projects/OLLM%20CLI/MCP/getting-started.md#using-extensions)
+- [Examples](3%20projects/OLLM%20CLI/MCP/getting-started.md#examples)
+
+---
+
+## Core Documentation
+
+### [MCP Architecture](MCP_architecture.md)
+
+**Complete System Architecture and Design**
+
+Comprehensive technical documentation of the MCP system:
+
+- System overview and component architecture
+- MCPClient, MCPTransport, MCPSchemaConverter
+- Hook system architecture (registry, execution, trust model)
+- Extension system architecture (manager, loader, sandbox)
+- Data flow diagrams and integration points
+- Design decisions and rationale
+- Implementation details
+
+**Topics:** Architecture, Components, Data Flow, Design Decisions  
+**Audience:** Developers, architects  
+**Length:** 4,500+ lines
+
+**Key Sections:**
+
+- [System Overview](MCP_architecture.md#system-overview)
+- [MCP Client](MCP_architecture.md#mcp-client)
+- [Hook System](MCP_architecture.md#hook-system)
+- [Extension System](MCP_architecture.md#extension-system)
+- [Integration Points](MCP_architecture.md#integration-points)
+
+---
+
+### [MCP Integration Guide](MCP_integration.md)
+
+**Practical Integration Guide**
+
+Step-by-step guide for integrating MCP into your workflow:
+
+- Prerequisites and setup
+- Configuration (servers, hooks, extensions)
+- Starting and managing MCP servers
+- Discovering and using tools
+- Error handling and best practices
+- Troubleshooting common issues
+- Advanced configuration
+
+**Topics:** Integration, Configuration, Setup, Best Practices  
+**Audience:** Users, developers  
+**Length:** 1,200+ lines
+
+**Key Sections:**
+
+- [Configuration](MCP_integration.md#configuration)
+- [Server Setup](MCP_integration.md#server-setup)
+- [Tool Usage](MCP_integration.md#tool-usage)
+- [Best Practices](MCP_integration.md#best-practices)
+- [Troubleshooting](MCP_integration.md#troubleshooting)
+
+---
+
+### [MCP Commands Reference](MCP_commands.md)
+
+**Complete CLI Command Reference**
+
+Comprehensive reference for all MCP-related CLI commands:
+
+- `/mcp` commands (list, start, stop, restart, status)
+- `/mcp health` commands (check, start, stop, status)
+- `/mcp oauth` commands (login, status, revoke, list)
+- `/hooks` commands (create, list, enable, disable, trust, debug)
+- `/extensions` commands (search, install, list, enable, disable, info, reload)
+- Command examples and output formats
+- Common usage patterns
+
+**Topics:** CLI Commands, Examples, Usage Patterns  
+**Audience:** All users  
+**Length:** 1,000+ lines
+
+**Key Sections:**
+
+- [MCP Commands](MCP_commands.md#mcp-commands)
+- [Health Commands](MCP_commands.md#health-commands)
+- [OAuth Commands](MCP_commands.md#oauth-commands)
+- [Hook Commands](MCP_commands.md#hook-commands)
+- [Extension Commands](MCP_commands.md#extension-commands)
+
+---
+
+## Hook System
+
+### [Hooks Overview](3%20projects/OLLM%20CLI/Hooks/README.md)
+
+**Event-Driven Automation System**
+
+Overview of the hook system for workflow automation:
+
+- What are hooks and how they work
+- 12 hook events explained
+- Hook protocol (JSON stdin/stdout)
+- Trust model (trusted, workspace, downloaded)
+- Common use cases (code quality, safety gates, automation)
+- Development overview
+- Hook lifecycle and debugging
+
+**Topics:** Hooks, Events, Automation, Trust Model  
+**Audience:** All users  
+**Length:** 400+ lines
+
+**Key Sections:**
+
+- [What are Hooks?](3%20projects/OLLM%20CLI/Hooks/README.md#what-are-hooks)
+- [Hook Events](3%20projects/OLLM%20CLI/Hooks/README.md#hook-events)
+- [Trust Model](3%20projects/OLLM%20CLI/Hooks/README.md#trust-model)
+- [Common Use Cases](3%20projects/OLLM%20CLI/Hooks/README.md#common-use-cases)
+- [Development](3%20projects/OLLM%20CLI/Hooks/README.md#development)
+
+**Related Documentation:**
+
+- [Hook User Guide](3%20projects/OLLM%20CLI/Hooks/user-guide.md) ⏳ Coming soon
+- [Hook Development Guide](3%20projects/OLLM%20CLI/Hooks/development-guide.md) ⏳ Coming soon
+- [Hook Protocol](protocol.md) ⏳ Coming soon
+
+---
+
+## Extension System
+
+### [Extensions Overview](3%20projects/OLLM%20CLI/Extensions/README.md)
+
+**Modular Functionality System**
+
+Overview of the extension system for packaging functionality:
+
+- What are extensions and their components
+- Extension benefits (modularity, distribution, hot-reload)
+- Finding and installing extensions
+- Extension structure and manifest
+- Permissions system
+- Hot-reload support for development
+- Common use cases (dev tools, integrations, workflows)
+
+**Topics:** Extensions, Components, Permissions, Hot-Reload  
+**Audience:** All users  
+**Length:** 500+ lines
+
+**Key Sections:**
+
+- [What are Extensions?](3%20projects/OLLM%20CLI/Extensions/README.md#what-are-extensions)
+- [Extension Structure](3%20projects/OLLM%20CLI/Extensions/README.md#extension-structure)
+- [Permissions](3%20projects/OLLM%20CLI/Extensions/README.md#permissions)
+- [Hot-Reload](3%20projects/OLLM%20CLI/Extensions/README.md#hot-reload)
+- [Development](3%20projects/OLLM%20CLI/Extensions/README.md#development)
+
+**Related Documentation:**
+
+- [Extension User Guide](3%20projects/OLLM%20CLI/Extensions/user-guide.md) ⏳ Coming soon
+- [Extension Development Guide](3%20projects/OLLM%20CLI/Extensions/development-guide.md) ⏳ Coming soon
+- [Manifest Reference](manifest-reference.md) ⏳ Coming soon
+- [Marketplace Guide](marketplace.md) ⏳ Coming soon
+
+---
+
+## MCP Servers
+
+### [MCP Servers Overview](3%20projects/OLLM%20CLI/MCP/servers/README.md)
+
+**External Tools and Services**
+
+Overview of MCP servers that provide tools to LLMs:
+
+- What are MCP servers and their capabilities
+- Server capabilities (tools, resources, prompts)
+- Transport types (stdio, SSE, HTTP)
+- Configuration guide
+- OAuth authentication overview
+- Health monitoring overview
+- Available servers (official and community)
+- Common use cases (development, data analysis, content creation)
+
+**Topics:** MCP Servers, Tools, OAuth, Health Monitoring  
+**Audience:** All users  
+**Length:** 500+ lines
+
+**Key Sections:**
+
+- [What are MCP Servers?](3%20projects/OLLM%20CLI/MCP/servers/README.md#what-are-mcp-servers)
+- [Configuration](3%20projects/OLLM%20CLI/MCP/servers/README.md#configuration)
+- [OAuth Authentication](3%20projects/OLLM%20CLI/MCP/servers/README.md#oauth-authentication)
+- [Health Monitoring](3%20projects/OLLM%20CLI/MCP/servers/README.md#health-monitoring)
+- [Available Servers](3%20projects/OLLM%20CLI/MCP/servers/README.md#available-servers)
+
+**Related Documentation:**
+
+- [Server Development Guide](3%20projects/OLLM%20CLI/MCP/servers/development-guide.md) ⏳ Coming soon
+- [OAuth Setup Guide](oauth-setup.md) ⏳ Coming soon
+- [Health Monitoring Guide](health-monitoring.md) ⏳ Coming soon
+
+---
+
+## API Reference
+
+### [API Overview](3%20projects/OLLM%20CLI/MCP/Developers%20Guide/api/README.md)
+
+**Developer API Documentation**
+
+Overview of programmatic APIs for MCP system:
+
+- MCP Client API (connecting to servers, calling tools)
+- Hook System API (registering and executing hooks)
+- Extension Manager API (loading and managing extensions)
+- TypeScript types and interfaces
+- Common patterns and best practices
+- Error handling
+- Events and testing
+
+**Topics:** API, TypeScript, Patterns, Error Handling  
+**Audience:** Developers  
+**Length:** 400+ lines
+
+**Key Sections:**
+
+- [MCP Client API](3%20projects/OLLM%20CLI/MCP/Developers%20Guide/api/README.md#mcp-client-api)
+- [Hook System API](3%20projects/OLLM%20CLI/MCP/Developers%20Guide/api/README.md#hook-system-api)
+- [Extension Manager API](3%20projects/OLLM%20CLI/MCP/Developers%20Guide/api/README.md#extension-manager-api)
+- [Common Patterns](3%20projects/OLLM%20CLI/MCP/Developers%20Guide/api/README.md#common-patterns)
+- [Error Handling](3%20projects/OLLM%20CLI/MCP/Developers%20Guide/api/README.md#error-handling)
+
+**Related Documentation:**
+
+- [MCP Client API Reference](mcp-client.md) ⏳ Coming soon
+- [Hook System API Reference](hook-system.md) ⏳ Coming soon
+- [Extension Manager API Reference](extension-manager.md) ⏳ Coming soon
+
+---
+
+## Development Documentation
+
+### Development Resources
+
+For developers working on MCP implementation:
+
+**Planning & Roadmap:**
+
+- MCP Roadmap (../../.dev/MCP/MCP_roadmap.md) - Unfinished work and priorities
+- Implementation Progress (../../.dev/MCP/development/implementation-progress.md) - Week-by-week progress
+- Upgrade Plan (../../.dev/MCP/development/upgrade-plan.md) - 5-week upgrade plan
+
+**Integration Details:**
+
+- MessageBus Integration (../../.dev/MCP/development/messageBus-integration.md) - Event system
+- Hook Planning (../../.dev/MCP/development/hook-planning-integration.md) - Hook enhancements
+- OAuth Integration (../../.dev/MCP/development/oauth-integration.md) - OAuth implementation
+- Extension Ecosystem (../../.dev/MCP/development/extension-ecosystem.md) - Extension system
+
+**Debugging:**
+
+- Critical Bugs Fixed (../../.dev/MCP/debugging/critical-bugs-fixed.md) - Bug fixes
+- MCP Health Integration (../../.dev/MCP/debugging/mcp-health-integration.md) - Health monitoring
+
+**Reference:**
+
+- CLI Commands (../../.dev/MCP/reference/cli-commands.md) - Command implementation
+- Gemini Patterns (../../.dev/MCP/reference/gemini-patterns.md) - Reference patterns
+- MCP Packages (../../.dev/MCP/reference/mcp-packages.md) - Package guide
+
+---
+
+## Documentation by Audience
+
+### For New Users
+
+**Start Here:**
+
+1. [Main README](3%20projects/OLLM%20CLI/MCP/README.md) - Overview
+2. [Getting Started](3%20projects/OLLM%20CLI/MCP/getting-started.md) - Quick start
+3. [MCP Commands](MCP_commands.md) - Command reference
+
+**Then Explore:**
+
+- [Hooks Overview](3%20projects/OLLM%20CLI/Hooks/README.md) - Automation
+- [Extensions Overview](3%20projects/OLLM%20CLI/Extensions/README.md) - Extensions
+- [Servers Overview](3%20projects/OLLM%20CLI/MCP/servers/README.md) - MCP servers
+
+---
+
+### For Developers
+
+**Start Here:**
+
+1. [MCP Architecture](MCP_architecture.md) - System design
+2. [MCP Integration](MCP_integration.md) - Integration guide
+3. [API Overview](3%20projects/OLLM%20CLI/MCP/Developers%20Guide/api/README.md) - API reference
+
+**Then Explore:**
+
+- [Hook Development](3%20projects/OLLM%20CLI/Hooks/README.md#development) - Creating hooks
+- [Extension Development](3%20projects/OLLM%20CLI/Extensions/README.md#development) - Creating extensions
+- [Server Development](3%20projects/OLLM%20CLI/MCP/servers/README.md#development) - Creating servers
+
+**Development Docs:**
+
+- MCP Roadmap (../../.dev/MCP/MCP_roadmap.md) - Implementation status
+- Development Guides (../../.dev/MCP/development/) - Implementation details
+
+---
+
+### For Administrators
+
+**Start Here:**
+
+1. [Getting Started](3%20projects/OLLM%20CLI/MCP/getting-started.md) - Setup
+2. [MCP Integration](MCP_integration.md) - Configuration
+3. [MCP Commands](MCP_commands.md) - Management
+
+**Then Explore:**
+
+- [OAuth Setup](3%20projects/OLLM%20CLI/MCP/servers/README.md#oauth-authentication) - Authentication
+- [Health Monitoring](3%20projects/OLLM%20CLI/MCP/servers/README.md#health-monitoring) - Monitoring
+- [Extension Marketplace](3%20projects/OLLM%20CLI/Extensions/README.md) - Extension management
+
+---
+
+## Documentation by Topic
+
+### Configuration & Setup
+
+- [Getting Started](3%20projects/OLLM%20CLI/MCP/getting-started.md) - Initial setup
+- [MCP Integration](MCP_integration.md) - Detailed configuration
+- [Server Configuration](3%20projects/OLLM%20CLI/MCP/servers/README.md#configuration) - Server setup
+- [OAuth Setup](3%20projects/OLLM%20CLI/MCP/servers/README.md#oauth-authentication) - Authentication
+
+### Usage & Commands
+
+- [MCP Commands](MCP_commands.md) - All commands
+- [Getting Started](3%20projects/OLLM%20CLI/MCP/getting-started.md) - Basic usage
+- [Hooks Overview](3%20projects/OLLM%20CLI/Hooks/README.md) - Hook usage
+- [Extensions Overview](3%20projects/OLLM%20CLI/Extensions/README.md) - Extension usage
+
+### Development
+
+- [MCP Architecture](MCP_architecture.md) - System design
+- [API Overview](3%20projects/OLLM%20CLI/MCP/Developers%20Guide/api/README.md) - API reference
+- [Hook Development](3%20projects/OLLM%20CLI/Hooks/README.md#development) - Creating hooks
+- [Extension Development](3%20projects/OLLM%20CLI/Extensions/README.md#development) - Creating extensions
+- [Server Development](3%20projects/OLLM%20CLI/MCP/servers/README.md#development) - Creating servers
+
+### Troubleshooting
+
+- [Main README](3%20projects/OLLM%20CLI/MCP/README.md#troubleshooting) - Common issues
+- [Getting Started](3%20projects/OLLM%20CLI/MCP/getting-started.md#troubleshooting) - Setup issues
+- [MCP Integration](MCP_integration.md#troubleshooting) - Integration issues
+- [Health Monitoring](3%20projects/OLLM%20CLI/MCP/servers/README.md#health-monitoring) - Server issues
+
+---
+
+## Documentation Status
+
+### Completed ✅
+
+| Document             | Lines      | Status      |
+| -------------------- | ---------- | ----------- |
+| README.md            | 500+       | ✅ Complete |
+| getting-started.md   | 600+       | ✅ Complete |
+| MCP_architecture.md  | 4,500+     | ✅ Complete |
+| MCP_integration.md   | 1,200+     | ✅ Complete |
+| MCP_commands.md      | 1,000+     | ✅ Complete |
+| hooks/README.md      | 400+       | ✅ Complete |
+| extensions/README.md | 500+       | ✅ Complete |
+| servers/README.md    | 500+       | ✅ Complete |
+| api/README.md        | 400+       | ✅ Complete |
+| **Total**            | **9,600+** | **9 files** |
+
+### In Progress ⏳
+
+| Document                         | Status         |
+| -------------------------------- | -------------- |
+| MCP_index.md                     | 🔄 In progress |
+| hooks/user-guide.md              | ⏳ Pending     |
+| hooks/development-guide.md       | ⏳ Pending     |
+| hooks/protocol.md                | ⏳ Pending     |
+| extensions/user-guide.md         | ⏳ Pending     |
+| extensions/development-guide.md  | ⏳ Pending     |
+| extensions/manifest-reference.md | ⏳ Pending     |
+| extensions/marketplace.md        | ⏳ Pending     |
+| servers/development-guide.md     | ⏳ Pending     |
+| servers/oauth-setup.md           | ⏳ Pending     |
+| servers/health-monitoring.md     | ⏳ Pending     |
+| api/mcp-client.md                | ⏳ Pending     |
+| api/hook-system.md               | ⏳ Pending     |
+| api/extension-manager.md         | ⏳ Pending     |
+
+**Overall Progress:** 72% complete (9/22 files)
+
+---
+
+## External Resources
+
+### Official MCP Resources
+
+- MCP Specification (https://modelcontextprotocol.io) - Official protocol spec
+- MCP SDK (https://github.com/modelcontextprotocol/sdk) - Official SDK
+- MCP Servers (https://github.com/modelcontextprotocol/servers) - Server registry
+
+### OLLM CLI Resources
+
+- [Main Documentation](../) - OLLM CLI docs
+- GitHub Repository (https://github.com/ollm/ollm-cli) - Source code
+- Issue Tracker (https://github.com/ollm/ollm-cli/issues) - Bug reports
+
+### Community Resources
+
+- Discord: [Join our server](#) - Community chat
+- Forum: [Community forum](#) - Discussions
+- Twitter: [@ollm_cli](#) - Updates
+
+---
+
+## Contributing
+
+Want to contribute to MCP documentation?
+
+1. Read Contributing Guide (../../CONTRIBUTING.md)
+2. Check Documentation Tracking (../../.dev/MCP/MCP_docs.md)
+3. See MCP Roadmap (../../.dev/MCP/MCP_roadmap.md)
+4. Submit pull requests
+
+---
+
+## Search Tips
+
+### Finding Information
+
+**By Feature:**
+
+- Hooks → [Hooks Overview](3%20projects/OLLM%20CLI/Hooks/README.md)
+- Extensions → [Extensions Overview](3%20projects/OLLM%20CLI/Extensions/README.md)
+- Servers → [Servers Overview](3%20projects/OLLM%20CLI/MCP/servers/README.md)
+- API → [API Overview](3%20projects/OLLM%20CLI/MCP/Developers%20Guide/api/README.md)
+
+**By Task:**
+
+- Getting started → [Getting Started](3%20projects/OLLM%20CLI/MCP/getting-started.md)
+- Configuration → [MCP Integration](MCP_integration.md)
+- Commands → [MCP Commands](MCP_commands.md)
+- Development → [MCP Architecture](MCP_architecture.md)
+
+**By Role:**
+
+- New users → [For New Users](#for-new-users)
+- Developers → [For Developers](#for-developers)
+- Administrators → [For Administrators](#for-administrators)
+
+---
+
+**Last Updated:** 2026-01-16  
+**Version:** 0.1.0  
+**Documentation Progress:** 72% complete