ugh, i keep my apps in ~/Applications so as to keep the systemwide /Applications not needed to be backed up. Then I just back up $HOME/. The problem is if I exclude $HOME from spotlight indexing, it won't let me command-space launch apps in ~/Applications. I'd happily make an /Applications.mine or something but you can't make directories in the root of osx anymore because the root is readonly and all user data is on an overlay fs.