When you click on the Prepare > Javascript menu option, your liturgical website javascript file (app.js) will open in an editor. Use the editor to make modifications. You must manually save the file after making changes.
In your doxa/sites directory, you can have one or more named sites. For each named site, there is an app.js file in the doxa/sites/{sitename}/assets/js directory.
Javascript is a programming language that is executed by a web browser. It provides actions to a website, e.g. something happens when you click a button. Most people will not need to modify the javascript for the their generated liturgical website. But, if you need to, you can.
Do not edit the javascript file unless you know what you are doing!
You can also edit the app.js file using any text editor that is installed on your computer.