If you want to use mage.exe alone, what you need to know is that it cannot be done. At least not with mage.exe alone. Mage.exe does not have a way to build a deployment manifest (*.application file) to download *.deploy files. You must manually edit the deployment manifest (*.application file) before signing it. Specifically, you need to add the mapFileExtensions attribute to the deployment XML element.
As an example suppose you have an executable named ClickOnceText.exe in a folder named 1.0.0.0., here is what you do:
> mage -n Application -t 1.0.0.0\ClickOnceTest.exe.manifest -fd 1.0.0.0 -cf ..\code.p12 -pwd passwd ClickOnceTest.exe.manifest successfully signed > mv 1.0.0.0\ClickOnceTest.exe 1.0.0.0\ClickOnceTest.exe.deploy > mage -n Deployment -t ClickOnceTest.application -appm 1.0.0.0\ClickOnceTest.exe.manifest ClickOnceTest.application successfully created > notepad ClickOnceTest.applicationAnd here is the trick. Add the mapFileExtensions to the deployment element:
<deployment mapFileExtensions="true" ... >
And then sign the deployment manifest (*.application).
> mage -u ClickOnceTest.application -cf code.p12 -pwd passwd ClickOnceTest.application successfully signed
With this information, you should be able to write a script to do your deployment with mage.exe. Of course, you will need a way to edit the deployment manifest (*.application) XML file, from your scripting language. But that would be the topic of another post.