We ran into this yesterday when discussing Everparse with Tahina.
The makefile for the 3D modules tests failed to rebuild the test when you changed the 3d file.
There were duplicate config.json files for the VS Code extension in the source tree. Particularly the one in src/3d was problematic, because it reset the include path. As a result, the extension did not work on fst files generated by the tests. (This change does not depend on https://github.com/FStarLang/fstar-vscode-assistant/pull/30 in any way.)
We ran into this yesterday when discussing Everparse with Tahina.