What exactly is part of an application depends on its code management scheme. In the simplest scheme it will at least consist of an application folder in which it runs and in which its specific reside. But usually it will also have an application classFolder, which is a direct subfolder of the root classFolder (classes) and has the same name as the application folder.
An application may have its domain classes in its own classFolder, or in another classFolder. It may also share that classFolder with another application. This is defined in index.php in the application folder. These classes may include other classes from whatever classFolder. As far as these classes are specific to the application they belong to the application as well.
Finally an application may use several style sheets, script files and image files. These are considered to be part of the application too. You have to decide for yourself how you keep track of them. We suggest you use files and folders with the same name as your application to make that easier.
For example, this example 11 is a phpPeanuts application running in the folder named 'example11'. It has an application class folder whose path (relative to the classes folder) is '', holding user interface classes. It shares its domain classes with example 4, whose classes are in ''. It uses a style sheet (example11.css) and several images from the 'example11/media' folder that are also considered part of the application.