I'll try to explain better. There are applications that came on CDs. Pop the CD in the CD tray and some of them install (install.exe) and then do not need the CD anymore to run the application. Some you need to run install.exe, and they partially install but need the CD to access some of the application features. Some of the applications have an exe file that runs the content on the CD - it does not install so the whole file structure can be copied to the hard drive and run directly from the harddrive without the CD, so yes, those are the ones that copy the contents locally and provide a shortcut so that the users don't need to carry around the CDs.
Although everything installed and worked perfectly, after the app layer was finalized, there was nothing but empty folders.