Modernize codebase with CLI improvements, structured configuration, and enhanced logging

[Copilot]

Comprehensive modernization of the BioPyAssistant codebase focusing on better maintainability, configuration management, and developer experience.

Configuration & Data Management

• Introduced YAML-based configuration for course chapters and metadata, replacing hardcoded directory paths
• Added Pydantic models for settings validation and type safety
• Centralized prompt management in external text files for easier iteration

CLI & Tooling

• Migrated to Click for command-line interfaces with pathlib.Path support
• Added configurable embedding model and provider options to create_database
• Enhanced create_database with chapter IDs and improved chunk metadata (file_path, file_name)

Logging & Developer Experience

• Implemented structured logging module with file and stdout output
• Added detailed chunk metadata examples in logs for debugging
• Extended markdown header renumbering to support level 5 headers

Dependency & Code Cleanup

• Updated LangChain imports for compatibility with latest versions
• Removed unused Gradio dependency and obsolete scripts
• Improved docstrings and fixed typos across modules
• Configured pre-commit hooks for code quality

Streamlit UI

• Simplified footer with LLM and prompt settings display
• Enhanced chatbot application logging

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