@marcrasi Thanks for your advice on how to debug the problem!
With Vapor, it turned out that some of module.modulemap's contain relative paths to headers, so when the file is copied to /tmp/xxx it stops working.
Another problem with modulemaps you’ve mentioned occurs because swift does not place local dependency into the .build folder of fake jupyterInstalledPackages package, and the code that copies modulemap files doesn’t know where to look for them.
I was able to fix both issues by 1) reading list of dependencies’ modulemaps from .build/build.db file and 2) replacing all relative headers paths with absolute when copying modulemaps.
Here’s commit, if you think this approach is adequate I can open PR.