Most recent changes as of 9-1-14

At this point I had a function in PermutationAndIsotopyClasses
(BothOps.m) which takes in a representative of an isotopy class and
applies both operations. The documentation in these files can explain
more.

After both operations are performed on order 5 squares all 50 squares
were created meaning there are two isotopy classes but it requires two
operations to produce all the normalized squares.