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I use the Ctrl+g keybinding to retrieve mail from my POP mail server. Whenever I do this, Mutt will ask me if I want to delete messages from the server.

If I tell it "no", it will download all of the messages from the server over again, resulting in duplicate messages in my inbox.

If I tell it "yes", it deletes everything from the server.

I need to be able to access my emails on different devices, but I don't want to go through the hassle of downloading every single email over and over again whenever I check my email. Is there any way to get around this?

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This answer provides a way to remove/delete duplicate emails in mutt email client. At present I myself still am unaware how to prevent the duplicate email download in the first place. Anyway this is how to at least remove the clutter:

Since the sequence of commands might be not straight-forward, here a recipe list:

  1. Set mutt to display/sort messages according to thread: press o and then select t for thread.
  2. Once in thread mode you can tag(=select/mark) the dupplicate copies of messages via: T and then inputing the pattern =~. As a result all duplicate copies should have a * for displaying them as currently tagged
  3. Now input ;d to mark the duplicates messages deleted. Depending on you configuration the messages will be presented with a D (for deleted) in front of them, or even be gone directly
  4. If set deleted D you still need to purge the messages from the maildir. This purging of the D marked messages can be achieved hitting $ which saves the changes to the maildir file/folder. It will ask you to confirm the deletion of the messages.

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