Configuration files must be associated with a deployable, which means you need at least 1 deployable in your application. Some of the differences between a deployable and an application are highlighted in this article: http://inedo.com/support/kb/1032/the-difference-between-deployables-and-applications For now, just create a deployable with the same name as your application and then you'll be able to create a config file.

FYI we have released a new version of the DotNetRecipes extension, if you update that extension within BuildMaster then re-create the example app, the signing should work correctly. As for the certificate hash problem, that has been resolved in the .NET extension which is scheduled for a release later today or early tomorrow.

All you should need to do is copy the output to wherever you want it published using the "Transfer Files" action immediately following the "Prepare ClickOnce Application".