What I do: Publishing .Net 3.5 application via VS, or msbuild (whatever), and now I need to insert to the published application separate directory (Modules - not added as a reference to the project - our project architecture does not allow this). So I'm copying the folder to published location then runs mageUI.exe select the application manifest and then the problems starts. As I press the populate button it's adding also hidden directory? So I remove the directory, after I want to save the manifest file I get the "Warning MSB3110: Assembly 'NAME.Shell.application.deploy' has mismatched identity 'NAME.Shell.application', expected file name: 'NAME.Shell.application.application'".

Did you have the same problems, according to http://smartclient.codeplex.com/Project/Download/FileDownload.aspx?DownloadId=5060 it should be easy as 1-2-3 but it's not.