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For example, if I played a game and downloaded some game contents in the app and then saved some game progress, there should be some files generated within the app. After syncing with iTunes, where will those information be stored?

I could find the appname.ipa file in iTunes Music folder, but that's the same app file downloaded from iTunes. For the app files generated after I used it, where will they be stored?

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I don't think the actually files are copied, but the backup directory for iDevices is ~/Library/Application Support/MobileSync/Backup

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There is a Mac app called Mobile Sync Browser that will attempt to parse the backup files and show what is in them. Look under "AppDomain" for any material from apps.

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