After JDK-8292944, we only generate module-deps.gmk once at the start of Init.gmk. This causes `make clean <some other target>` to first generate and then remove module-deps.gmk after which the rest of the build proceeds without a module-deps.gmk, causing problems with dependencies.

Simple reproducer that quickly demonstrates the problem:
$ make clean interim-langtools

Workaround for users is to run "clean" separately before building again.