start arguments refactoring
add arguments for optimzation
stan_args not using find_index
arguments refactor almost done
fix part of read_stan_csv for arg_refactor
update example csv files
fix traceplot when no warmup sample
add some doc for new arguments (not finished)
fix issue #11: sample_file does not work for optim
fix issue #11 2, no sample_file for optim
more doc for new argument scheme
fix stan-dev/stan issue #205
Merge branch 'feature/arg_refactor' into develop

Conflicts:
	rstan/example/testoptim.R