Meanwhile it's also a "who cares?" problem for the npm people. They don't use this OS, and don't expect ever to do so.
I think the node_modules directory structure is a novel, though straightforward, solution to the problem of interdependent module versioning. It's very Unix; it reminds me a bit of GNU stow. It makes perfect sense that it will be tweaked in the new npm to be less redundant, but it only really makes sense to tweak systems that already work perfectly. (Otherwise they should be fixed first, then tweaked.) Certainly it's better than having a separate LD_LIBRARY_PATH setting for every command invocation! (even that doesn't fix everything...)
It doesn't even seem like an obvious solution to the problem. Take Maven for instance: a global dependency repository under which the dependencies are stored in the form <groupId>/<artifactId>/<version>. If X depends on Y.1 and Z depends on Y.2, so what? You have all the dependencies stored on your filesystem in a relatively flat structure.
If I had coded in Java on Windows for years, I wouldn't trust my sense of what's "obvious". I'm not too impressed by a "global" repository either. Python struggled against that stupid architecture for years before they got virtualenv in good working order. Node just took a shortcut to the future.
"All direct dependencies are in the node_modules directory, full-stop" is a pretty simple rule. Really, that's the only rule, and that's all of it. You don't need to worry about second-order dependencies, because those are direct dependencies of some other module, which means... they are in that module's node_modules directory.
I think the node_modules directory structure is a novel, though straightforward, solution to the problem of interdependent module versioning. It's very Unix; it reminds me a bit of GNU stow. It makes perfect sense that it will be tweaked in the new npm to be less redundant, but it only really makes sense to tweak systems that already work perfectly. (Otherwise they should be fixed first, then tweaked.) Certainly it's better than having a separate LD_LIBRARY_PATH setting for every command invocation! (even that doesn't fix everything...)