When you run and deploy your application using CUBA Studio or gradle the build system will bundle your components according to the configuration in polymer.json file. By default it will bundle the whole application into a single app-shell.html file. When you change some of your app components Studio will hot deploy it to the tomcat. Also it will replace bundled app-shell.html with unbundled version in order changes to be picked. Keep it in mind if you deploy your application on production directly from tomcat/webapps.