In my experience the problem you're identifying there is an general failing to understand boundaries when designing the system. A language or framework shouldn'

In my experience the problem you're identifying there is an general failing to understand boundaries when designing the system. A language or framework shouldn't pervade every package, to aid this in my most recent large project we formulated a naming structure for packages that gave an indication of where they fit in, from a high level perspective, and the sorts of dependencies they should have.