Yeah, I'm not seeing how "tree node_modules" is an argument against npm per se. Maybe one could argue npm, inc promotes the small-modules approach, but I don't think that's relevant to whether npm itself is a good package manager.
No matter whether you think small modules are good or bad, I personally have experienced npm to at least manage them well. Admittedly, however, I've never actually worked on projects of any great size.
Yeah, of course. But it's something like using a Dvorak keyboard layout -- every time you use another computer or help someone else you hit friction. Customizing system level key binding is something I've intentionally avoided.
I hadn't! I just started writing React last week, and coming from writing Swift it feels more wild-westy. Of course, that's how I felt going from Java to Objective C long before Swift came around, so I'm sure I'll get used to it. Nice to know about these kinds of things though!
No matter whether you think small modules are good or bad, I personally have experienced npm to at least manage them well. Admittedly, however, I've never actually worked on projects of any great size.