The /assets/js/custom-script.js allows you to override plugin functions within AppStrap as well as add your own plugin definitions using AppStrap to load in the theme assets.

You can also use the AppStrap Javascript API to react to javascript events in AppStrap:

1. themePreload: Before any AppStrap Javascript has run
2. themePrePlugins: Before any AppStrap Javascript has run
3. themeLoaded: After the theme has loaded everything
4. themePluginsExtras: Add new plugin integrations or override existing ones.

See assets/js/custom-script.js for example code.