Add include paths to src_info, update stanc3 argument handling

[WardBrian]

Submission Checklist

• Run unit tests
• Declare copyright holder and open-source license: see below

Summary

Closes #516 by adding include paths if they exist.

Updates compiler_opts to reflect that allow_undefined and include_paths are being replaced by allow-undefined and include-paths respectively. We emit a warning and use the non-deprecated versions.

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):
Simons Foundation

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)

[mitzimorris]

lgtm!