Feature/issue 405 refactor command

#### Summary:

Started refactoring command so it can be shared.

#### Intended Effect:

Started refactoring src/stan/gm/command.hpp.
- CmdStan is in its own repository.
- command in gm namespace moved to namespace common.
- added typedef `stan_model` in generated model

#### How to Verify:

Run all tests. The CmdStan tests are now in the CmdStan repository.

#### Side Effects:

Stan no longer has CmdStan built into it. (It can still generate a main, but it's not meant to stay for much longer.)

#### Documentation:

The separation of CmdStan will need some documentation. Stan will no longer need to be downloaded.

#### Reviewer Suggestions:

Bob, Michael, or Jiqiang.