Recently I was experimenting with SharePoint 2013 Apps and different deploy possibilities. I made a few changes on the linked projects, changed some project and solution settings and out of a sudden the debugger did not work for my web project. No matter what I did, it just ignored the breakpoints and even exception did pop up in the Visual Studio. After searching a while I found the solution and it was so incredibly easy. When debugging SharePoint 2013 Apps both, the app and the web project, have to be set as start-up project. The solution property page should look like this: