Updates to CmdStan for the Stan refactor

[syclik]

Submisison Checklist

• Run tests: ./runCmdStanTests.py src/test
• Declare copyright holder and open-source license: see below

Summary:

Updates CmdStan to deal with changes with stan-dev/stan#2004.

This does not change behavior.

Intended Effect:

Refactoring of code. No changes to any behavior from the outside.

How to Verify:

All tests pass. Run any model with a seed and arguments. Results should be identical.

Side Effects:

Wait for stan-dev/stan#2004 to be merged before merging.

Documentation:

None.

Reviewer Suggestions:

Anyone.

Copyright and Licensing

Please list the copyright holder for the work you are submitting (this will be you or your assignee, such as a university or company): Columbia University

By submitting this pull request, the copyright holder is agreeing to license the submitted work under the following licenses:

• Code: BSD 3-clause (https://opensource.org/licenses/BSD-3-Clause)
• Documentation: CC-BY 4.0 (https://creativecommons.org/licenses/by/4.0/)