The server.js file has indeed been removed from the package. The solution is in the readme:
Setup
Install drupal-node.js packge with npm:
npm install drupal-node.js
Make sure to do this outside of your Drupal modules directory, else Drupal may try to process folders containing Node.js module information and fail. Follow the install instructions in the drupal-node.js NPM package. You will need to provide the hostname and port of your Drupal site to the Node.js process, and ensure that the service token matches between Drupal and Node.js.
I suppose they separated the server from the Drupal module to allow more frequent updates. The npm package contains a settings file and app.js, which includes server.js.
sudo apt-get install nodejsnot sure if for CentOS if it's the same.