Comment by jonpacker

I respect where you're coming from, but I disagree. One of the huge advantages of npm for me is that it's so transparent and I can see exactly how it's mapping to the file system. I know exactly which code is being run, from where—because it's incredibly easy to traverse the dependency tree. If you abstract away the fs level and flatten the dependencies into a single folder, you take this away, and you make the dependency tree essentially a big intimidating blob of code that requires slogging through package lists to determine what is actually being used.