Removing the proto directory and its file.
Removing the log4j properties and a bunch of package HTML files that are not needed.
Removing a few more files from the top-level directory that are not needed.
Removed some @Override annotations from the Cluster class.
Removing the @Override annotations from the Node class.
Removing the @Override annotations from the Zone class.
Removing the Action inferface from the project because we don't want any interfaces. Updating the imports in Pipeline accordingly.
Removing the @Override annotations from the ByteArray class.
Removing an interface and the method that used it from the Utils class.
Adding the findbugs and annotations jars from the findbugs project. These are needed (or at least the annotations is) when doing analysis because there is code that needs the javax.annotation.Nullable class.
Merge branch 'scenario1' into scenario1-s1

The scenario1 branch has been updated, so those changes need to be incorported here so that we can be working off of the same base. The small diff between scenario1-s1 and scenario1 needs to remain though.