Add more nuance to system module deps
Rather than eliminating all system module/bootclasspath deps, only
remove the auto-added deps and maintain those that are manually added.
Test: b run :bp2build_progress report \
-m core-lambda-stubs-for-system-modules and verify system_modules
dep is present
Change-Id: If783ce23245c56b268e86d08090258d516f59a09