Phase 3.3: Multi-objective optimization fix, updated docs & Claude skill

- Fixed drone gimbal optimization to use proper semantic directions
- Changed from ['minimize', 'minimize'] to ['minimize', 'maximize']
- Updated Claude skill (v2.0) with Phase 3.3 integration
- Added centralized extractor library documentation
- Added multi-objective optimization (Protocol 11) section
- Added NX multi-solution protocol documentation
- Added dashboard integration documentation
- Fixed Pareto front degenerate issue with proper NSGA-II configuration

🤖 Generated with [Claude Code](https://claude.com/claude-code)

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

README.md

@@ -31,11 +31,27 @@ Atomizer enables engineers to:
 
 ---
 
-📘 **For Developers**: See [DEVELOPMENT_GUIDANCE.md](DEVELOPMENT_GUIDANCE.md) for comprehensive status report, current priorities, and strategic direction.
+## Documentation
 
-📘 **Vision & Roadmap**: See [DEVELOPMENT_ROADMAP.md](DEVELOPMENT_ROADMAP.md) for the long-term vision and phase-by-phase implementation plan.
+📚 **[Complete Documentation Index](docs/00_INDEX.md)** - Start here for all documentation
 
-📘 **Development Status**: See [DEVELOPMENT.md](DEVELOPMENT.md) for detailed task tracking and completed work.
+### Quick Links
+
+- **[Visual Architecture Diagrams](docs/09_DIAGRAMS/)** - 🆕 Comprehensive Mermaid diagrams showing system architecture and workflows
+- **[Protocol Specifications](docs/PROTOCOLS.md)** - All active protocols (10, 11, 13) consolidated
+- **[Development Guide](DEVELOPMENT.md)** - Development workflow, testing, contributing
+- **[Dashboard Guide](docs/DASHBOARD.md)** - 🆕 Comprehensive React dashboard with multi-objective visualization
+- **[NX Multi-Solution Protocol](docs/NX_MULTI_SOLUTION_PROTOCOL.md)** - 🆕 Critical fix for multi-solution workflows
+- **[Getting Started](docs/HOW_TO_EXTEND_OPTIMIZATION.md)** - Create your first optimization study
+
+### By Topic
+
+- **Protocols**: [PROTOCOLS.md](docs/PROTOCOLS.md) - Protocol 10 (Intelligent Optimization), 11 (Multi-Objective), 13 (Dashboard)
+- **Architecture**: [HOOK_ARCHITECTURE.md](docs/HOOK_ARCHITECTURE.md), [NX_SESSION_MANAGEMENT.md](docs/NX_SESSION_MANAGEMENT.md)
+- **Dashboard**: [DASHBOARD_MASTER_PLAN.md](docs/DASHBOARD_MASTER_PLAN.md), [DASHBOARD_REACT_IMPLEMENTATION.md](docs/DASHBOARD_REACT_IMPLEMENTATION.md)
+- **Advanced**: [HYBRID_MODE_GUIDE.md](docs/HYBRID_MODE_GUIDE.md) - LLM-assisted workflows
+
+---
 
 ## Architecture
 
@@ -163,16 +179,18 @@ python run_5trial_test.py
 
 ## Features
 
-- **Intelligent Optimization**: Optuna-powered TPE sampler with multi-objective support
+- **Intelligent Multi-Objective Optimization**: NSGA-II algorithm for Pareto-optimal solutions
+- **Advanced Dashboard**: React-based real-time monitoring with parallel coordinates visualization
 - **NX Integration**: Seamless journal-based control of Siemens NX Simcenter
+- **Multi-Solution Support**: Automatic handling of combined analysis types (static + modal, thermal + structural)
 - **Smart Logging**: Detailed per-trial logs + high-level optimization progress tracking
 - **Plugin System**: Extensible hooks at pre-solve, post-solve, and post-extraction points
 - **Study Management**: Isolated study folders with automatic result organization
 - **Substudy System**: NX-like hierarchical studies with shared models and independent configurations
 - **Live History Tracking**: Real-time incremental JSON updates for monitoring progress
 - **Resume Capability**: Interrupt and resume optimizations without data loss
-- **Web Dashboard**: Real-time monitoring and configuration UI
-- **Example Study**: Bracket displacement maximization with full substudy workflow
+- **Pareto Front Analysis**: Automatic extraction and visualization of non-dominated solutions
+- **Parallel Coordinates Plot**: Research-grade multi-dimensional visualization with interactive selection
 
 ## Current Status