npm command to uninstall or prune unused packages in Node.js

If you're not worried about a couple minutes time to do so, a solution would be to rm -rf node_modules and npm install again to rebuild the local modules.

Note: Recent npm versions do this automatically when running npm install if package-locks are enabled, so this is not necessary except for removing development packages with the --production flag.

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Run npm prune to remove modules not listed in package.json.

From npm help prune:

This command removes "extraneous" packages. If a package name is provided, then only packages matching one of the supplied names are removed.

Extraneous packages are packages that are not listed on the parent package's dependencies list.

If the --production flag is specified, this command will remove the packages specified in your devDependencies.