app.js is the "bundle". It is a concatenation of all your application's files into one.
Try running:
npm run build
and inspect the files generated at the /dist folder.
The files in the /dist folders are basically the output webpack produces when it builds your project. app.js itself, as said, is a concatenation of all your application's files (those written by yourself and maybe some third-party that you imported), after some transformations performed by plugins and webpack itself.