VASim needs minor refactoring

[jackwadden]

There is a lot of commented out "dead" code in VASim. There is also a lot of "method2()" left over from lazy feature addition and debug cycles. VASim needs a massive cleanup to make it easier to read, use, and add new functionality.

VASim also needs a cleaner way to safely manipulate automata graphs (e.g. adding edges between nodes etc...). Once added, this optimization and transformation algorithm should be refactored to use these cleaner functions.

Automata.cpp is also getting fairly bloated. It would be nice to separate out the optimizations into one file, the transformations into another file, and keep the getters/setters and other functionality inside the original file.

Feel free to propose other "refactors" that will help make the code base better.