Changes: updated makefile to use InputParser instead of input. used inputParser in Controller.initSystem instead of hacked together Main function. added fields to Controller such as snapshotTime, routingUpdateTime, hostsById, routersById. Changed all pointers to lists/maps to just lists/maps (see issues). implemented snapshotTime/routingUpdateTime setters. fully implemented initSystem to run and read an input file and create the objects (run takes a filename and passes it on to initSystem). slight change to make_plots.cpp to account for changes in Control design.