Avoid using package maker at all costs. Would you like to explain why you need to install your application in the first place? In most cases you should be able to fix it up so it doesn't need to...
The thing is, package maker has serious bugs in it, and when you install into multiple directories, permissions on things like / can easily get changed, which is a bad thing
Anyways, if you're sure you need to install, you can create something like ~/MyAppDist/ and inside that create an Applications and whatever, and then set the install root to /
i hope that makes sense
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