In my solution I have 3 projects, a Web, a Setup (build) and a Merge Module. The merge module contains 3rd part files. In my setup project on the file system I have a folder called scripts that I use to link the merge module to. I also have the default Web Application Folder that I use to get my Content and Primary output from. Everything builds correctly but when I deploy the MSI the files that should be placed in the Scripts folder that is created is instead put in the Web application root folder. This is not the behavior that I am expecting.