You don't need to stash deps in a subdirectory, IMHO that's a node.js design flaw that leads to tons of duplication. I don't think there's any other package manager for a popular language that works like this by default (Bundlers does allow you to version dependencies which can be useful for deployment, but you still only ever get one version of any dependency unlike node).

You just need to have some sort of wrapper/program that knows how to figure out which dependencies to use for a project. With bundler, you just wrap everything in "bundle exec" (or use binstubs).