Fixed all the integration issues with IOUtilities

I went through IOUtilities and fixed all the include issues and the
namespacing issues. Everything works and compiles on my system, and I
can run the program and get the environment x,y, and z dimensions.

In order to make the test program, enter the following command in the
root project directory:

g++ -I./ -Isrc -o bin/metrosim src/Applications/Application.cpp
src/Applications/Application.h src/Applications/CommandParsing.cpp
src/Applications/CommandParsing.h src/Metropolis/Box.h
src/Metropolis/Simulation.cpp src/Metropolis/Simulation.h
src/Metropolis/SimulationArgs.h src/Metropolis/SerialSim/SerialBox.cpp
src/Metropolis/SerialSim/SerialBox.h
src/Metropolis/Utilities/StructLibrary.cpp
src/Metropolis/Utilities/StructLibrary.h
src/Metropolis/Utilities/IOUtilities.cpp
src/Metropolis/Utilities/IOUtilities.h

After the program is built, run the demo by entering the following
command:

bin/metrosim stuff/demoConfiguration.txt