Second command-line argument to enforce original algorithm

[glwhart]

I'm not a fan of the current format for the second (optional) command-line argument: T or F. I'd rather have a descriptive keyword. Change this in the near future.

Also, the unit tests are broken with this change. Need to update the xml file for the unit tests.

[afonari]

I will be happy to change the name to whatever is desired.

[afonari]

Since the update to speed up the calculations (it is a great update). This flag became really useful since degeneracy is important for my computations.