docs: reorganize documentation structure and clean up examples

docs/INDEX.md

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+# BinarySniffer Documentation
+
+Welcome to the BinarySniffer documentation. This index will help you find the information you need.
+
+## Getting Started
+
+- **[Installation Guide](INSTALLATION.md)** - Step-by-step installation instructions for BinarySniffer
+- **[User Guide](USER_GUIDE.md)** - Complete guide to using BinarySniffer CLI and library API
+
+## Core Features
+
+- **[Detailed Features](DETAILED_FEATURES.md)** - Comprehensive overview of BinarySniffer's capabilities
+- **[Architecture](ARCHITECTURE.md)** - System architecture and design principles
+- **[Signature Management](SIGNATURE_MANAGEMENT.md)** - Managing and updating signature databases
+
+## Signature Creation
+
+- **[Creating Signatures](CREATING_SIGNATURES.md)** - Guide to creating new component signatures
+- **[Signature Creation](SIGNATURE_CREATION.md)** - Advanced signature creation techniques and best practices
+
+## Advanced Topics
+
+- **[ML Security Analysis](ML_SECURITY.md)** - Security scanning and analysis for ML frameworks
+- **[TLSH Fuzzy Matching](TLSH_FUZZY_MATCHING.md)** - Using TLSH for fuzzy hash matching
+- **[TLSH Setup Guide](TLSH_SETUP_GUIDE.md)** - Installing and configuring TLSH support
+
+## Reference
+
+- **[API Reference](API_REFERENCE.md)** - Python API documentation and examples
+- **[Package Verification](PACKAGE_VERIFICATION.md)** - Verifying BinarySniffer packages and integrity
+
+## Scripts and Examples
+
+- **[create_tlsh_example.py](create_tlsh_example.py)** - Example script for TLSH hash creation
+
+---
+
+## Quick Links
+
+### For New Users
+1. Start with [Installation Guide](INSTALLATION.md)
+2. Follow the [User Guide](USER_GUIDE.md)
+3. Explore [Detailed Features](DETAILED_FEATURES.md)
+
+### For Developers
+1. Review [Architecture](ARCHITECTURE.md)
+2. Check [API Reference](API_REFERENCE.md)
+3. Learn about [Signature Creation](SIGNATURE_CREATION.md)
+
+### For Security Analysis
+1. Read [ML Security Analysis](ML_SECURITY.md)
+2. Understand [TLSH Fuzzy Matching](TLSH_FUZZY_MATCHING.md)
+3. Configure with [TLSH Setup Guide](TLSH_SETUP_GUIDE.md)
+
+---
+
+## Getting Help
+
+If you need help or have questions:
+- Check the relevant documentation section above
+- Review the main [README.md](../README.md) in the project root
+- Report issues at [GitHub Issues](https://github.com/SemClone/binarysniffer/issues)