Allowed creating nodes with no weights.

This is useful for the input test layers.
Now processing the command line arguments.
Allowed for a larger number of layers.

The test inputs will need their own layers of neurons, albeit
without any weights.
Now have a way to load and persist a network.

Uses a definition file currently. Will also use an input file for
testing and running inputs in the future.
Moved files to directories to clean up workspace.
Fixed the makefile to build everything with new directories.