Fixed issue where renamed classes/methods referenced in a different dex file would not be renamed properly. Deobfuscation only modified the Class info for the InfoStorage of the Dex file the class belonged to. If a class in another Dex file referenced it, it would not know of the rename.

This commit moves InfoStorage to the RootNode. This allows all classes to know of each other regardless of the Dex file. A dexId field was added to the DexNode class to allow the the MethodInfo.fromDex function to continue to use method index to locate methods. The getMethod and putMethod functions in InfoStorage was modified to take a DexNode. The DexNode id is used to create a unique key used for the lookup into the methods HashMap.