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you might be able to do it in place, like this: $ for m in Mail/{cur,new}/*; do echo $m; procmail <$m; rm $m; done You have to remove each original email afterwards, or else procmail will duplicate it. It will also record everything as new. I'm not sure of a good way to handle that.

The alpine program does not support Maildir format mailboxes out of the box, although there is a patch floating around out there somewhere that adds this feature. If you're using Maildir, you can use mutt, which works great with maildir folders, or you can set an IMAP server (e.g., dovecot) that supports Maildir, and then configure alpine and other mail ...