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

You could remove your node_modules/ folder and then reinstall the dependencies from package.json.

rm -rf node_modules/
npm install

This would erase all installed packages in the current folder and only install the dependencies from package.json. If the dependencies have been previously installed npm will try to use the cached version, avoiding downloading the dependency a second time.

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