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Close this up if you feel like I am trolling (which I am) :) No offence taken and I apologize! Just thought that given the cutting edge nature of bioinformatics, you may want to help think of ways to push the boundaries of how we use Node.js :)
There is not an easy alternative to NPM as of yet, but the idea is the main point. Why not just source a package from where ever you please? Instead of a "node_modules" folder at the root, offer a "modules" folder instead. NPM ends up limiting the names people can use and could be described as a cumbersome process. Just about every NPM package is a GitHub repo anyway, why not cut out the middle man.
It would be amazing if there was a simple schema that allowed you to source packages from Git over ssh, http servers and local file systems. To follow the UNIX philosophy well there is likely a few separate projects would have to spin out of the idea. I just feel that eventually NPM has to go, or any body which claims an amount authority as to what stays and goes.
For inspiration there are these projects...
https://github.com/duojs/duo (this is really focused on the browser, but the core idea is key)
https://github.com/ismotgroup/bring (the concept of replacing "require" with an alternative is really the point here)
Thanks!