Created folders for all files

Made the repository look like a repository. Took way too much time.
New files dividing the Wire serialization

All these files represent the changes made to divide the wire serialization.
The resulting files are a little easier to understand.
Include changes for header helper with new folders
Final changes to files for folder changes.

Had to delete extensions/nnnSIM/model/wire/nnnsim/nnnsim.cc because I divided
into the wire/nnnsim/ folders. All the other changes are for the includes in
the files.

Yey