Sorry, I don't want to seem negative - but it seems to me that maybe you haven't used Espruino that much yet, and you're trying to apply the lessons you learned on million-line enterprise projects to a device that can handle maybe 10k lines maximum?
It's not to say they're not good ideas - but the reality is that NPM for Node.js is a necessity because of the amount of different libraries people tend to pull into their projects. On Espruino we haven't even hit the stage where version control is a minor annoyance yet.
At the moment, I think <10 people have contributed modules to Espruino. Keeping the modules together means I can be a lot more sure that they're of good quality and all work with Espruino, and I think that's a real bonus when compared to something like Arduino and Node.js where you have 5 different libraries which all do the same thing.
At some point we'll reach the stage where I can't keep track of everything, and then yes, NPM will make a huge amount of sense. But until then I think switching over to NPM may not actually be in everyone's best interests.
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