The current problem is that I have to specify the location of the module like var module = require('./node_modules/xyz/lib/xyz.js'). But then electron does not find the dependencies of xyz, which are located within ./node_modules/xyz/node_modules/yyy and complains ./yyy.js can not be found.
The electron app structure
dist  
├── angular2.dev.js   
├── config.js  
├── index.html  
├── main.js  
├── node_modules  
├── package.json  
└── app.js