Feature/refactor stan command

This pull request updates the Stan submodule to develop. In Stan, src/stan/gm/command.hpp has moved to src/stan/common/command.hpp and some of the functions were broken out.

In addition to the refactoring, there is a new make target to run C++ unit tests on RStan itself. That target is test-cpp.

Let me know if you want additional tests showing that the behavior is identical between the old RStan and the current RStan.