A long time ago I wrote the Manifest Manager Utility to make it easier to edit ClickOnce manifests for composite application scenarios where the application DLLs are not all directly referenced by the shell application. That code was updated for the release of SCSF 2010, but unfortunately a late breaking change in the framework caused that version to stop working with .NET 4.0 RTM.
The Prism team has taken ownership of that utility from SCSF, and we updated it to work with .NET 4.0. The new version is now available on CodePlex here. Thanks much to Robin Shahan (@robindotnet) for pointing out the fix.
The utility makes it easy to open both the deployment manifest and application manifest of a ClickOnce app at the same time in a single editor to do things like update the publish version, add and remove files, change the application name or the deployment location (provider). Saving saves and signs both manifests in one action, saving the hassle of trying to do everything in the right order across two manifests. You can see the UI here.