you have a package.json file that shows the main configuration of your project, and a lockfile that contains the full details of your project configuration such as the urls that holds each of the package or libraries used in your project at the root folder of the project......
npm is the default package manager for Node.js....
All you need to do is call $ npm install from the terminal in the root directory where you have the package.json and lock file ...since you are not adding any particular package to be install ..... it will go through the lock file and download one after the other, the required packages from their urls written in the lock file if it isnt present in the project enviroment .....
you make sure you edit your package.json file .... to give an entry point to your app..... "name":"app.js" where app.js is the main script .. or index.js depending on the project naming convention...
then you can run..$ Node app.js or $ npm start if your package.json scripts has a start field config as such "scripts": { "start": "Node index.js", "test": "test" }..... which is indirectly still calling your $ Node app.js