Remove unnecessary Python files from repo

[yiquintero]

Description

A list of all the Python files in the the tudatpy repo was created with the purpose of determining which files should be:

• included in the API docs
• kept, but not included in the API docs
• removed from the repo

Solution

It was determined the following files in the tudatpy repo should be removed from the repo:

• bodies/*
• cli/*
• apps/*
• elements.py
• prototype.py

[DominicDirkx]

@yiquintero Have these removals been made part of one of the PRs that you opened, or are they still to be done?

[yiquintero]

These files have been removed as part of the tudatpy project reestructuring. The only files that remain are the ones inside the cli directory, which are now located in tudatpy/temp/cli.