Alright, so you want to use the Generic Bootstrapper to deploy your application but for one reason or another you aren't using ClickOnce or a SetupProject. (You are developing a VC++ app with a custom installer, for example). Well, unfortunately there is no designer support ouf of the box but you still can create a Bootstrapper for your application. How?
The same way Visual Studio does, MSBuild of course!
There is no magic to creating a Bootstrapper, it is just an MSBuild target which ClickOnce and SetupProjects call for you. However, you don't have to leave all the Bootstrappin' fun to Visual Studio. Below is an example MSBuild file for creating a Generic Bootstrapper:
<!-- Include the 'Product Code' for every package you want -->
ApplicationName="My Awesome Application"
That's it! Now save that XML to a file, "CLI Bootstrapper Test.xml" for example, and on the command type:
MSBuild "CLI Bootstrapper Test.xml"
MSBuild will parse your target file, do a little magic, and *POOF* your very own private Bootstrapper.