How do I prevent prerequisite files from being duplicated in the app deployment folder?

Answer 1

One thing you can do is roll your own prerequisites using the Bootstrapper Manifest Generator. Set the URL to the location where you want to serve up the deployment. Then set the option in VS to "download from vendor location".

It will download the deployment from the URL you set in the BMG, and won't deploy the prerequisites each time you publish the ClickOnce application.