User manual

Working on the ipython user manual. Updating to actual markdown.
New version of the user manual

The iPython user manual is set up pretty well currently. It works with the tracpy code and runs a simple example that can be easily expanded and played around with.
Updated README.md file with accurate instructions
Added __init__, small doc fix to plotting, tools

Added an __init__.py file with some information about tracpy and tracmass.