Documented ciphers package

Methods in the ciphers package have been documented. Bug still exists
in the hill cipher class. Not sure what the issue is.
GUI

No changes made just recompilied.
Fixed a bug in the AdjMatGraphPlus

Bug was stopping us from correctly using our code map. Fixed BFS method
to work for our purposes. Other bugs in AdjMatGraphPlus may exist but
aren't a priority of ours.