Coded the connections from stim to cones

The bar stimulus class places a particular bar movie (from
RuntimeBarGenerator) onto the retina.  The cone layer connects to the
bar stimulus, but I still need to visualize the weights and activity to
verify everything works.
Cone Layer Works Slowly
Time enhancements in cone layer

The stimulus now holds intensity values instead of RGB values, so the
cones do no have to calculate it on the fly.
Horizontal layer diffusion
Cone and horizontal layers

Finished the cone and horizontal layer implementations
The retina now stores copies of the activities of the cone and
horizontal layers, and the retina can play back the activities in a
basic GUI (left/right arrow keys to move in time)
Cleaned up and commented most of the code, so it shouldn't make anyone's
eye's bleed.