How to clean node_modules folder of packages that are not in package.json?

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I think you’re looking for npm prune

npm prune [<name> [<name ...]]

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.

See the docs: https://docs.npmjs.com/cli/prune

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