You need to get the Bootstrapper Manifest Generator. This is from Brian
Noyes's blog. He wrote a ClickOnce book (an excellent and thorough
reference, by the way, and well worth the money):
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In my ClickOnce book, I talk about David Guyer's excellent tool for creating
Bootstrapper manifests for a custom bootstrapper item for your ClickOnce
deployed applications. The URL I gave in the book is no longer valid, the
BMG has been moved to codeplex at the following address:
http://www.codeplex.com/bmg
Basically, this tool gives you a nice dialog driven interface on the XML
manifest files that make it so you can just check a box in Visual Studio
(the Publish tab of project properties, Prerequisites button) to select your
custom installers to be included in the bootstrapper setup.exe that is
generated by ClickOnce.