Changing the way the parse_*_args functions work to take parameters struct as input. Better for multi_param
Better commandline for MFPT
Better commandline for FFTbor2D
Fixing 3 bugs. (1) argv[0] in each subparam is the subparam name. This fakes out getopt (otherwise it doesn't parse right.) (2,3) subparam argv flags are prefixed with a '-' and terminated with '\0'
Multiparam is working (see RNApopulation)