Code Overhaul

My portion of the code overhaul, adding the changes to make it more
extensible and the needed changes to the implemented classes.
Minor Tweaks

Made a few small changes before we merge the two branches.
Merge branch 'master' of https://github.com/Flatscan/MALTHUS

Conflicts:
	src/malthus/GCP/GCPIndividual.java
	src/malthus/GCP/GCPPopulation.java
	src/malthus/Gene.java
	src/malthus/Individual.java
	src/malthus/Population.java
	src/malthus/SimpleGene.java