My ClickOnce installation fails with an error:
File, WindowsFormsProject.exe, has a different computed hash than specified in manifest.
You can configure the signing process of the assembly and the ClickOnce manifest from VisualStudio:
All these settings will be valid when you build using MsBuild.
Note: You can generate your self-signed certificate from that screen if required.
Note 2: Remember that you have TWO manifests "Application Manifest" and "Deployment Manifest" both must be signed with the same certificate.
If you need to re-sign your manifests at any time after the build you can use Mage.exe.