Update Stan packaging for R-Devel compat

[andrjohns]

Summary:

The workflows for R-devel are currently failing. R is getting a bit stricter with the handling of .Rbuildignore - items specified there are no longer available during package build. This breaks the current approach of using cleanup scripts to copy the headers/sources when packaging.

This PR works around this by keeping the stan submodule(s) in the src folder and using .Rbuildignore to keep only the minimum needed sources when packaging.

In order to keep within the 100-character path limit when packaging, I've split the stan submodule into separate stan and math. If this approach seems like the way to go, I'll also update the Jenkins process for syncing the two modules.

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): Andrew Johnson

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

• Code: GPLv3 (https://opensource.org/licenses/GPL-3.0)
• Documentation: CC-BY 4.0 (https://creativecommons.org/licenses/by/4.0/)

[jgabry]

Thanks @andrjohns! @bgoodri what do you think about this approach?

[bgoodri]

Yeah, we are going to have to do something like this when we update StanHeaders for RcppEigen.