The app assumes that all entities and VOs are living in the same folder, which is never going to be the case.
The easiest way to do this is for the app to open a root folder, do a scan of all the VOs config files, then figure out their locations. Then other VOs can reference each other, even if they're in different folders. I think this makes the most sense, and it allow for a surprising amount flexibility.
This will require some surgery to the app, I think it makes sense to add this as a step in the pipeline, rather than iterating through them one by one, it does each batch per stage.