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(Unsound transform) Remove instances of missing submodules.
In our ordinary transformation process, e.g., vl-simplify, modules that instance an undefined submodule are thrown out with fatal errors.
In vl-lint, we still want to analyze them as much as we can. So, in this transformation, we simply delete any instances of missing submodules, perhaps leaving us with "partial" superior modules.
This is obviously unsound and should never be used in our ordinary transformation process.