Use `include_paths` in subdirectories for pre-compiled models

[jgabry]

Submission Checklist

• [ ] Run unit tests
• [x] Declare copyright holder and agree to license (see below)

Summary

Fixes #1094.

This does seem to fix #1094, but marking it as a draft PR for now. I need to add a test and to check a bit more whether this is the best way to fix this and whether this change affects anything that isn't covered by our current tests (we do have tests for includes, but they were missing this case so maybe are missing other cases that this affects).

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/)