>The issue I have is that I don't really have a good idea for a solution to this problem - on one hand, I don't expect everyone to roll the entire modern stacks by hand every time. Killing collaborative software development seems like literally throwing the baby out with the bath water.

Is NPM really collaborative? People just throw stuff out there and you can pick it up. It's the least commons denominator of collaboration.

The thing that NPM is missing is trust and trust doesn't scale to 1000x dependencies.