Removed the weird extraneous clean and cluster commands, simplified parsing structure.
Added deprecation warning to the cluster module
Removed cluster import from trajectory module.
Removed the extra scrape level of imports.
Moved the engines directory up a level to the trajectory package.
Removed the crunchbang for trj, since it's accessed via bash script now.
Fixed minor import bug.
Created directory from wrong variable.
Moved clean functionality into the purge argument of the trajectory module.