Many updates to paradox package, especially addition of functions to facilitate capturing and plotting output

I've also redone the paradox_sim_R.r function to match the C++ one. See /demo/diagnose-manipulate.r for a rough version of a diagnostic plot. Note that you'll need the foreach package and the doParallel package. The simulations are run on multiple cores now.

Still not plotting the time series... need to think about what to plot exactly. I.e. where on the 2d surface do you pick to plot the time series from?