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Saving of notes may be confusing for user: when I opened my PDF after I made notes they was there, so I thought that they've been saved in the document. It was "nice" surprise when after reinstallation of system I didn't found them in my PDF. If user sees his notes after he reopened PDF he will think that they saved in the document - it's dangerous misconception. Notes shouldn't be saved somewhere in the system until he saved them explicitly, so he will not think that he shouldn't save anything.