Well, for example, you may want to have a registry that only has approved 
modules outside of the public NPM registry (see --registry config in NPM 
and associated auth methods). Also you may want to set user who is running 
the NPM script (--user). Finally, you may want to set various other config 
options (npm help config) for other more specialized needs.

Remember, NPM does allow shell access during installations, and you may not 
want to always use the defaults if you do not know the origin of the script.

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