StuntsPT/Structure_threader: 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