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Microsoft runs a certain way, using a certain code, and figuring things out with certain logistics. Other programs are similarly unique. However, Microsoft also uses it's processes to interface with other programs. By installing say, a game, without the add or remove programs option, you're forcing the computer to abide by the games code. If you use the tool, you're making the game blend with the computer's code. As for removal, it simply ensures that registry files and other such things are cleaned/removed.

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