As I have just completed a huge pure Nodejs project in 80+ files I had the same problem as OP. I needed at least a minimal protection for my hard work, but it seems this very basic need had not been covered by the NPMjs OS community. Add salt to injury the JXCore package encryption system was cracked last week in a few hours so back to obfuscation...
So I created the complete solution, that handles file merging, uglifying. You have the option of leaving out specified files/folders as well from merging. These files are then copied to the new output location of the merged file and references to them are rewritten auto.
NPMjs link of node-uglifier
Github repo of of node-uglifier
PS: I would be glad if people would contribute to make it even better. This is a war between thieves and hard working coders like yourself. Lets join our forces, increase the pain of reverse engineering!
require('../mylib/lib1')
) – Compensation