sim output now writes to a separate folder for each sim within raw_sim_output; added specn.gradient and specn.factor to params.out output
added set.seed(sim) so that replicate simulations should be exactly duplicatable by different users
fixed creation of output subdirectory
check to make sure subdirectory doesn't already exist before creating it; also updated test_sim to use sim.id (and seed) 9999, and therefore changed all of the test values accordingly
added stopCluster(cl) to local==T case