When you create a new project it's good practice to have a folder structure that allows you to have a common code base for the view (i.e., HTML/CSS/JS) separated from specific platform folders and plugins.

The Apache Cordova community is vibrant and there is a project on GitHub named cordova-cli that you can use to create a folder structure that makes it easy to build, debug, and emulate cross-platform mobile apps. For more information and to get the source code, go to https://github.com/apache/cordova-cli.