Yes, you can do this.
Just create a folder manually inside app folder and instantiate the classes whenever required by calling it with requires : [].
example usage :
requires: ['MyApp.service.primeService']
include the above line in app.js where MyApp is the application name and service is the custom folder, primeService is the custom js file.
app.js might be as follows :
Ext.application({
name: 'MyApp',
appFolder: 'app-demo',
extend: 'Ext.app.Application',
requires: ['MyApp.service.primeService'],
launch: function(){
//code here
}
})