Make problem files into functions so we can pass in command-line arguments to it (like instance number).
Make sure eigenspectrum data or plots aren't outputted for all T's if doing a multi-T simulation.
Several changes. Changed problem file params for probs and outputs, probshow and probout specify output to screen and output to file respectively. State labels and final state probabilities are NOT sorted unless they're being printed out to screen. This is so that we can keep all probability vector orderings consistent and save disk space (we don't have to store the labels but once, probs can be stored alone). All other outputs have the option of outputting to binary as well by specifying the binary option variable in the problem file.
Updated the readme mostly.
Updated all problem files to conform to the new problem file being a function format. Also put some of the plotting scripts in tools/.