added lib back into tracked folders
added nauty related gitignore
cleaned up DreadNautRuntime
moved stuff to edu.wisc.cs.amalgam package
removed old methods
cleaned up Tuple.java
removed Instances.java
cleaned up Instance.java
MAJOR refractor for NautyHashMethod - stuff is now static
removed unused imports
Got rid of TupleList.java
made it SUPER FAST
removed traces - for now