chore: codebase audit and fixes (ruff, mypy, pytest)

Fix codebase issues: linting, types, tests, and security.

Production Upgrade v2.0: SSE streaming, HIPAA compliance, Gradio Q&A UI

Deploy to HuggingFace Spaces - Medical RAG with vector store

Refactor: Improve code quality, security, and configuration

docs: update all documentation to reflect current codebase state

refactor: major repository cleanup and bug fixes