How can I protect a ClickOnce deployed application with a password? Do I have to change the IIS settings of the web or is there a way to do it programmatically?
A ClickOnce installer is just a couple installer files sitting out on your web server, right? So then, you can just implement some sort of directory security on those files. You can do this on a couple different levels I believe; for example IIS permissions or (if your users are on your domain) NTFS permissions.
Also, IIS permissions (everything actually?) should be able to be setup programatically.