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.
Nothing in what I'm doing prevents what you like about npm. In fact npm already abstracts away what you want in a little known command called `npm explore`.
Let's say you want to explore the dependency `foo` in your project. At the root of your project type `npm explore foo` and press enter and you'll be in a shell exploring the foo module. Then if you want to return, type `exit` and return and you'll be back in your project. Or if you want to go down the rabbit hole to a dependency of foo called bar, type `npm explore bar` and press enter.
`npm explore` is a great way to explore things and navigate to the dependencies used by the dependency you want to investigate. It basically uses the information in the current package.json to find the dependency you want.
