Enhance README with AI/RAG Implementation Guidance

[HiteshSingh21]

This PR adds a section to the README.md about machine-readability and LLM integration.
As genomic data compliance tools move toward automated verification (e.g., the RegBot project), developers need clearer guidance on connecting traditional semantic logic with modern RAG-based pipelines.

Changes Included -

• Vector Search & DAG Warning
Explains how DUO’s Directed Acyclic Graph (DAG) hierarchy should be resolved before using vector databases, to avoid incorrect similarity calculations.
• Flat File Indexing
Recommends using the lightweight duo.csv file for system prompts and vector indexing instead of the heavier .owl ontology files.

Justification (Governance Alignment) -

• Simplicity – Points developers to the most practical files for NLP and indexing.
• Machine-readability – Helps automated tools interpret DUO constraints without requiring manual ontology parsing.

Contributor:
Hitesh Singh (GSoC '26 Applicant)