initial working of custom cost function ability
preferred nomenclature
handle default case of cost function smartly in optimizePath
standardize variable names in the new paradigm.
standardize chooseComponents to just treat overlap optimization as a special case of cost optimization.
only output threshold info if custom threshold is defined.
don't need to clear classes in example
mlint messages
examples don't need to close all figures, and use obscure figure numbers.
include example showing the custom cost function ability.