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I find it hard to believe it is all one file so to speak. I am sure underneath the hood it has files roaming around. In fact, I was fairly certain I read tech support issues where people did have to dig down to find some small files to do certain tweaks.
Applications do tend to be just one file with an installer pointing to it. The file in turn creates preference files elsewhere on the disk to store settings for the app. Sytem wide settings are a pain, sometimes there are stored in one of the control panels, other times they are hidden in an app that apple made. Ever try changing the default e-mail application in OSX 10.3? Can be a major pain to find these things.
There are library files for some applications which require pre-binding, in a terminal window do "man update_prebinding"
