How to maintain node_modules and packages dependencies clean using npm?

What are you doing when you use npm and maintain your node_modules clean? I am always annoyed with the packages dependence becomes messy and node_modules gets bloated when I install various libraries or plugins using npm (without thinking deeply).

I always try following commands...

$ npm outdated (check updates)

$ npm update Some-Package (update)

$ npm dedupe (simplify dependencies)

$ npm prune (delete unnecessary packages)

then

$ npm Init

I would like to let you know if there are other recommended methods or practice such as this. Thank you.

via HKudo