Make JSON input the default option

[rok-cesnovar]

In order to fix #96 we reverted back to using Rdump for the cmdstan input. Now that @mitzimorris has fixed the underlying Cmdstan issue that was the root of #96, we should move back to using JSON as the default input option.

We can do it after the release of 2.22 on the 18th January. We could do it now, but that would mean that those affected by this issue would need to use a git clone of cmdstan.