After updating Phoenix to 1.3.0 app.js was not loaded properly anymore. I got the error module js/app not found although js/app was loaded. e.g. confirm: "Sure?" option doesn’t work with my delete-buttons.

Thanks to cohawzk’s comment at Phoenix 1.2.x to 1.3.0 Upgrade Instructions I learned to update Brunch. Everything works fine again. Thank you cohawzk!

# assets/packages.json
"devDependencies": {
   "babel-brunch": "~6.0.0",
-  "brunch": "2.7.4",
+  "brunch": "2.10.7",
   "clean-css-brunch": "~2.0.0",
   "css-brunch": "~2.0.0",
   ...

$ cd assets
$ npm install
$ cd ..
$ mix phx.server