In my application, I load some assemblies dynamically, depending on what was the user's choice. Naturally, these are not referenced in the project. When publishing with ClickOnce, these assemblies are not included in the package.
The question is - is it possible to trick the ClickOnce publisher to use some other files not referenced in the project?
I assume you are using Visual Studio to publish the deployment.
If you want to continue this way, you will either have to add the files as references, or add them as content to the project. Under the properties of the start-up project, go to the publish tab, Application Files.., and make sure the file is included.
Your other option is to build and publish the click-once manifests outside of Visual Studio using mageui.exe (or mage.exe if you want to work from the command line).
An alternative to MageUI is ManifestManagerUtility for ClickOnce.