You could reorder your folder structure simply by dragging and dropping. If you drag and drop your imported js folder to your main folder, a message would be prompted whether you like to overwrite your original js folder.
I am also glad to say that with the current version of Icenium you could rename your Workspace or Project. So if you want to change the application identifier you could rename your Project folder, which is the folder on the second level of hierarchy. When you rename it using the context menu and redeploy your application the application identifier would be changed to the new project name.
All the best,
the Telerik team
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