Bells and whistles

Lots of changes in this new release.

• Implemented improved logging (with colors!)
• The arguments are now split between run and plot
  • There were plenty of changes to the way arguments are handled, so this will break backwards compatibility.
• Lots of plotting fixes
• Improved sanity checks stop the user from entering input file errors
• General bugfixes and interface polish.

This is a .0 version, so please report any bugs you find.