Technical improvements

[kpedro88]

• Refactor the main function in run_model to be importable
• Reorganize the assembly of Pythia lines in svjHelper so that all physically-related lines (e.g. anything for the Z′ mediator) are set in the same part of the code (or at least a more logically simple progression of functions in the code)
• Handle subfolders in a more consistent way
• Make Plots.py configurable