All source files show "This file is not part of any project" for generic imported project.

I have a large custom Qt Creator project created using the "Import Existing Project" functionality.
When I open the project in Qt Creator 4.10.1 or today's nightly build, I can see all of the project source files in the the "Projects" side bar. However, whenever I open a source file from the sidebar, I get a message at the top of the editor that reads "Warning: This file is not part of any project. The code model might have issues parsing this file properly."

Sure enough, none of the included header files can be located (despite their directories being present in the project's ".includes" file) and thus the editor window is a sea of errors.

If I open the same project in Qt Creator 4.8.2, it works fine, so this appears to be a regression.