major refactoring:

[PedroMTQ]

The purpose of this PR is to overhaul the codebase via multiple steps:

• improve architecture and class inheritance (e.g., better procedure separation)
• re-organizing codebase for clearer role separation
• change installation method to avoid relying on extra scripts for installation of tools; poetry was also added for better distribution

The goal of this PR is not to add new features, instead all features should be preserved and entry points should remain the same.