Code refactor (Physics)

[Sinclert]

This PR refactor the Python code for the Physics use-case (docker-images-physics/code).

The refactor includes nice additions like:

• Relative paths: allowing scripts configurate.py and generate.py to be run locally (debug). Other scripts depends on the _mgpythia REANA step.
• Standarized code blocks: most scripts present a similar structure:
  • Definition of global variables.
  • Argument parsing.
  • Configuration loading.
  • Custom steps...
  • Saving a particular file.

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In addition, some cleanup has been performed as the entire _code/mgprocesses folder is auto-generated when running the generate.py script. It has been removed from the repository, and its name added to the .gitignore.

Same action has been taken with the code/data, logs and software folders.

[irinaespejo]

This is great thank you so much!