You could pretty easily re-write your comment and say "Look at the trails Debian + apt have blazed. That's the right move."
https://github.com/rubygems/rubygems
http://dominictarr.com/post/25516279897/why-you-should-never...
http://dontkry.com/posts/code/modules-the-right-way.html
To be more specific, what npm does that pip, debian, and rubygems don't do is nested dependencies, which is a wonderful advancement.
https://github.com/rubygems/rubygems