Refactor architecture to follow object-oriented class structure

[harryswift01]

Restructure the codebase to adopt a consistent and maintainable object-oriented architecture. This involves encapsulating related functionality into cohesive classes, improving separation of concerns, and organizing the system around clear responsibilities.

• Identify procedural or loosely grouped functions and organize them into appropriate classes.
• Define core classes (e.g. LevelManager, EntropyManager, RunManager) with clear ownership of responsibilities.
• Introduce private attributes and encapsulate internal state (_attribute pattern).
• Use @property decorators to expose only necessary parts of the internal state.
• Replace global/shared variables with instance attributes where appropriate.
• Ensure each class has a single, clear purpose (Single Responsibility Principle).
• Refactor duplicate or ambiguous function names for clarity and alignment with class behavior.
• Ensure reusable logic (e.g. matrix generation, entropy calculations) is encapsulated in class methods rather than procedural scripts.
• Remove or refactor legacy code that violates OOP principles.