We also restructured the grammars of the EMF-IncQuery project about a year ago. I don't remember exactly what was needed to manage the generation into the new package, but one of the following had to do the trick:
- We have moved the mwe and xtext files into a new package.
- This meant, we had to update the grammarURI property in the MWE
- We have updated the grammar/ecore uri to be similar to the new naming convention.
All our changes are available in our old repository (https://github.com/ujhelyiz/EMF-IncQuery/commit/6f7a618fc7f89386c9f85b3481761168ea91857a), but I cannot provide a smaller example. You might want to look for the Xtext, MWE, and possibly manifest changes.