Refactor 2zone_skimming.py script

[aletzdy]

This issue opens up the task to refactor the 2zone_skimming.py script. This script carries out the MGRA-level skimming whose outputs are used throughout the model.

The goal of this task is to revise the code for better readability and maintainability. The result of this task is a modularized python code, commented with explanations as needed.