Shadows, and Shadows-based ReadyThemes, ship with the Messages extension included. The CSS is part of /themes/%STORE_ID%/THEME_NAME/extensions.css and the JavaScript is in /themes/%STORE_ID%/THEME_NAME/extensions.js. If you want to make styling changes, it is recommended you add them to your /themes/%STORE_ID%/THEME_NAME/theme.css file. The HTML for this extension can be accessed by navigating to User Interface -> Theme Components -> Content Sections -> messages.
If you are using Shadows DE, you can modify the CSS or JavaScript in build/extensions/messages/ and update as part of your build process.