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Clean Up does a number of things, including:
  • Removes items which do not match the current view settings from the view
  • Moves items out of the Inbox to their destination, if project and context match the conditions specified in the Data preferences
  • Refreshes the view
In no case does Clean Up actually remove items from the database, but it may hide them from sight. When you complete an action or project, it is simply marked complete, and although it may disappear from sight, it is not deleted.

Clean Up is done when you press cmd-K or the Clean Up toolbar button, use Edit→Clean Up, or switch views.