cd ./node_modules/library
npm install
npm run build

cd ../../app
npm install
npm run build

./app/dist/app.js now contains multiple jquery modules. That is probably the same behavior as node ./app/src/index.js because there are two jquery modules (./app/node_modules/jquery and ./node_modules/library/node_modules/jquery).

But since ./node_modules/library/webpack.config.js has externals: ["jquery"] I do not except ./node_modules/library/node_modules/jquery to be resolved by webpack.