Release v1.3.1: Complete Documentation & Interface Overhaul ✨ Major Features: - Comprehensive CLI parameter documentation with all v1.3.1 features - Complete elimination of documentation redundancies - Streamlined mkdocs navigation structure - Professional documentation standards implementation 🔧 Technical Improvements: - Full version synchronization across all pipeline components - Enhanced CITATION.cff with current metadata - Cleaned repository structure with orphaned file removal - Updated validation scripts and manifest documentation 📚 Documentation Enhancements: - Complete parameter reference including --invert_individual, --invert_means, --prepare_jbrowse_batch - Unified getting-started experience - Professional changelog and version tracking - Comprehensive usage documentation This release focuses on documentation quality and user experience improvements while maintaining full backward compatibility with existing workflows.