MAGE: Is used for creation and editing of the deployment manifests for your projects. If you use Visual Studio Pro or Ultimate, you can always add a deployment project to your solution and the manifest can be created automatically, but sometimes you have to edit the manifest, and this is the way to do it.
You can do the MAGE editing at the command line, using a batch process (the way you want to schedule the modifications) and by using a GUI editor.
When you want to use this? One thing is that you might a bunch of customers inside your company that require very customized installations, you could then set up a batch file to do this prior to deploying your application to the custom customers.
You can also use MageUI.exe, a graphical application, instead of Mage.exe. For more information, see MageUI.exe (Manifest Generation and Editing Tool, Graphical Client).
Also, don’t confuse it with this type of MAGE: