updated the change cli arguments

Removed commented out code and updated the --help messages for the command line tool.

some more updates to the terminal tool inputs.

Fixed the command line tool so that now the densities file is created. Here is an example of the line to run:

Merge refactored branch into main

Updated instructions in root readme for running and setup.

updated main.py to work.

Added setup instructions to the root readme.

removed duplicate plotting module and updated a case sensitive bug in main.py.

Removing duplicate code and old legacy data files

Transform project into proper Python package structure

Improve code quality with linting fixes and add Sphinx documentation

added unit tests, added doc strings and doc tests.

Remove debug statements from main.py and making_densities_file.py

Fix timestep argument parsing with proper default value