The way that we resolved this issue was to create a shell exe that as the one that was installed and deployed initially to the client machines.
The "real" executable program is stored in a subdirectory of this initial app. When the shell app is launched, after it has downloaded and installed any updates for the real app, it launches the real app's executable in a separate AppDomain.
Here is the core of the "real" app launching from within the shell app:
System.AppDomainSetup oSetup = new System.AppDomainSetup();
string sApplicationFile = null;
// Use this to ensure that if the application is running when the user performs the update, that we don't run into file locking issues.
oSetup.ShadowCopyFiles = "true";
oSetup.ApplicationName = sAppName;
// Generate the name of the DLL we are going to launch
sApplicationFile = System.IO.Path.Combine(sApplicationDirectory, sAppName + ".exe");
oSetup.ApplicationBase = sApplicationDirectory;
oSetup.ConfigurationFile = sApplicationFile + ".config";
oSetup.LoaderOptimization = LoaderOptimization.MultiDomain;
// Launch the application
System.AppDomain oAppDomain = AppDomain.CreateDomain(sAppName, AppDomain.CurrentDomain.Evidence, oSetup);
oAppDomain.SetData("App", sAppName);
oAppDomain.SetData("User", sUserName);
oAppDomain.SetData("Pwd", sUserPassword);
oAppDomain.ExecuteAssembly(sApplicationFile);
// When the launched application closes, close this application as well
Application.Exit();
Note that in our version, the shell app collects the user name and password from the user in order to access the update web site correctly. This data is then passed to the "real" app through the SetData
method on the AppDomain.