Integrate run script into Makefile

Now do "make ARG=<mode> run", or omit ARG to default to mode 2 (naive GPU).
Change 2D and 3D arrays to 1D

Indexing will need to be adjusted within the kernel. New input parameters have
been added to all kernels for row start pointers so that the out, delta,
weight, and prevWdt can be sparse matrices.