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

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

fix: all 15 bugs + full agentic RAG pipeline in HF Space

feat: Enable 100% HF Space capability with dynamic environment variables

Fix: Dynamic API key loading - secrets now work properly on HuggingFace Spaces

Refactor: Improve code quality, security, and configuration

docs: update all documentation to reflect current codebase state

refactor: major repository cleanup and bug fixes