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Org-mode does not maintain TODO lists as a separate document. TODO items are an integral part of the notes file, because TODO items usually come up while taking notes! With Org-mode, you simply mark any entry in a tree as being a TODO item. In this way, the information is not duplicated, and the entire context from which the item emerged is always present when you check.
Of course, this technique causes TODO items to be scattered throughout your file. Org-mode provides methods to give you an overview over all things you have to do.