fix: correct broken documentation links in README.md and docs/INDEX.md

README.md

@@ -38,7 +38,6 @@
 
 - **Node.js 18+** (LTS recommended)
 - **npm 9+** or equivalent package manager
-- **Windows users**: See [Windows Installation Guide](./docs/windows-installation.md) for special instructions
 
 ⚠️ **IMPORTANT**: Claude Code must be installed first:
 
@@ -201,7 +200,7 @@ claude mcp add flow-nexus npx flow-nexus@latest mcp start
 **Performance Tools:**
 - `benchmark_run`, `performance_report`, `bottleneck_analyze`
 
-📚 **Full Reference**: [MCP Tools Documentation](./docs/MCP-TOOLS.md)
+📚 **Full Reference**: [MCP Tools Documentation](./docs/reference/MCP_TOOLS.md)
 
 ---
 
@@ -287,26 +286,19 @@ npx claude-flow@alpha memory query "microservices patterns" --reasoningbank
 ## 📚 **Documentation**
 
 ### **Core Documentation**
-- **[Installation Guide](./docs/INSTALLATION.md)** - Setup instructions
-- **[Memory System Guide](./docs/MEMORY-SYSTEM.md)** - ReasoningBank usage
-- **[MCP Tools Reference](./docs/MCP-TOOLS.md)** - Complete tool catalog
-- **[Agent System](./docs/AGENT-SYSTEM.md)** - All 64 agents
+- **[MCP Tools Reference](./docs/reference/MCP_TOOLS.md)** - Complete tool catalog
+- **[Agent System](./docs/reference/AGENTS.md)** - All 64 agents
 
 ### **Release Notes**
 - **[v2.7.0-alpha.10](./docs/RELEASE-NOTES-v2.7.0-alpha.10.md)** - Semantic search fix
 - **[v2.7.0-alpha.9](./docs/RELEASE-NOTES-v2.7.0-alpha.9.md)** - Process cleanup
 - **[Changelog](./CHANGELOG.md)** - Full version history
 
 ### **Advanced Topics**
-- **[Neural Module](./docs/NEURAL-MODULE.md)** - SAFLA self-learning
-- **[Goal Module](./docs/GOAL-MODULE.md)** - GOAP intelligent planning
-- **[Hive-Mind Intelligence](./docs/HIVE-MIND.md)** - Queen-led coordination
-- **[GitHub Integration](./docs/GITHUB-INTEGRATION.md)** - Repository automation
+_Documentation coming soon_
 
 ### **Configuration**
-- **[CLAUDE.md Templates](./docs/CLAUDE-MD-TEMPLATES.md)** - Project configs
-- **[SPARC Methodology](./docs/SPARC.md)** - TDD patterns
-- **[Windows Installation](./docs/windows-installation.md)** - Windows setup
+- **[SPARC Methodology](./docs/reference/SPARC.md)** - TDD patterns
 
 ---
 

docs/INDEX.md

@@ -75,14 +75,14 @@ Complete automation toolkit covering file operations, system management, GitHub
 ## 📚 Complete Documentation Suite
 
 ### 🏃‍♂️ Getting Started
-- **[README-NEW.md](../README.md)** - Complete project overview and quick start
-- **[DEPLOYMENT.md](DEPLOYMENT.md)** - Installation, setup, and production deployment
+- **[README.md](../README.md)** - Complete project overview and quick start
+- **[DEPLOYMENT.md](development/DEPLOYMENT.md)** - Installation, setup, and production deployment
 - **System Requirements**: Node.js v20+, 2GB RAM minimum, 8GB recommended
 
-### 🏗️ Architecture & Development  
-- **[ARCHITECTURE.md](ARCHITECTURE.md)** - System design, patterns, and scalability
-- **[DEVELOPMENT_WORKFLOW.md](DEVELOPMENT_WORKFLOW.md)** - Development process and best practices
-- **[API_DOCUMENTATION.md](API_DOCUMENTATION.md)** - Complete API reference and examples
+### 🏗️ Architecture & Development
+- **[ARCHITECTURE.md](architecture/ARCHITECTURE.md)** - System design, patterns, and scalability
+- **[DEVELOPMENT_WORKFLOW.md](development/DEVELOPMENT_WORKFLOW.md)** - Development process and best practices
+- **[API_DOCUMENTATION.md](api/API_DOCUMENTATION.md)** - Complete API reference and examples
 
 ### 🎯 Core Concepts
 - **Agent Management**: Spawn, coordinate, and monitor AI agents
@@ -285,28 +285,20 @@ docs/
 ### 🎯 **By User Type**
 
 #### 👨‍💻 **Developers**
-1. [Quick Start Guide](../README.md#-quick-start) - Get up and running in 5 minutes
-2. [SPARC Development](../README.md#-sparc-development-environment) - Structured development methodology
-3. [API Reference](API_DOCUMENTATION.md) - Complete endpoint documentation
-4. [Development Workflow](DEVELOPMENT_WORKFLOW.md) - Best practices and standards
+1. [Quick Start Guide](../README.md) - Get up and running in 5 minutes
+2. [API Reference](api/API_DOCUMENTATION.md) - Complete endpoint documentation
+3. [Development Workflow](development/DEVELOPMENT_WORKFLOW.md) - Best practices and standards
 
-#### 🏢 **DevOps/Operations**  
-1. [Deployment Guide](DEPLOYMENT.md) - Production deployment strategies
-2. [Architecture Overview](ARCHITECTURE.md) - System design and scaling
-3. [Monitoring Setup](DEPLOYMENT.md#monitoring--maintenance) - Health checks and metrics
-4. [Security Implementation](ARCHITECTURE.md#security-architecture) - Security best practices
+#### 🏢 **DevOps/Operations**
+1. [Deployment Guide](development/DEPLOYMENT.md) - Production deployment strategies
+2. [Architecture Overview](architecture/ARCHITECTURE.md) - System design and scaling
 
 #### 👑 **Technical Leaders**
-1. [System Architecture](ARCHITECTURE.md#system-overview) - High-level system design
-2. [Performance Metrics](../README.md#-performance-metrics) - Benchmarks and optimization
-3. [Swarm Intelligence](../README.md#-swarm-intelligence) - Distributed coordination strategies
-4. [Enterprise Features](DEPLOYMENT.md#production-setup) - Production-grade capabilities
+1. [System Architecture](architecture/ARCHITECTURE.md) - High-level system design
+2. [Performance Metrics](../README.md) - Benchmarks and optimization
 
 #### 🚀 **Product Managers**
-1. [Feature Overview](../README.md#-key-features) - Complete capability matrix
-2. [Use Cases](../README.md#-use-cases) - Real-world applications
-3. [Integration Capabilities](../README.md#-integration-capabilities) - Platform compatibility
-4. [Roadmap](../README.md#-roadmap) - Future development plans
+1. [Feature Overview](../README.md) - Complete capability matrix
 
 ### System Requirements