spindle simulation with separate control, model, view

The simulation still runs via spindle_simulation (top level), which now acts as a controller. It takes in user variables (which the user right now has to change by hand), then hands these off to runModel.m, which runs the model and returns the results. Then, spindle_simulation.m can optionally plot the results.

To be implemented: a mechanism to save the important results. Also, a mechanism to compare a model (meaning, certain constants) to experimental results to obtain an error estimate. Later, this can be used to set up a genetic algorithm to find good constants.