I\'m making an installer for an OS X application, but have trouble understanding PackageMaker\'s UI. My version of PackageMaker is 3.0.4, running along Lion and Xcode 4.1.>
Given the case where the payload (i.e. source item to be installed) is Confused.app (which presumably contains a Contents subfolder with Info.plist, MacOS, Resources, etc inside that), and the install destination is /Applications:
The intended usage with "Include root.." disabled is that you'd create a proxy Applications folder on your build machine, designate that as the payload source, and place the app into that folder. This is more useful if you're installing multiple apps at once, or installing to places other than /Applications (i.e. make a proxy root folder, create Applications and Library/Application Support subfolders, and set the install destination as "/").