1) Added Comments and JavaDoc comments for the methods is Graph Class
and also to other methods inside other classes.

2) Added the cache class and this is not used yet. Just a skeleton.

3) YET TO COME - *** The Index on the Cache ***

4) DO NOT use the "SequentialDual.java". USE DualSimulation.java - its
more efficient and stable.

5) The Graph Signature method, Polytree method etc etc are all in the
Graph Class.