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From: Greg Troxel <gdt@work.lexort.com>
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Subject: Re: move article, agent does not expire ?
Date: Tue, 02 Oct 2007 07:55:12 -0400
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  But when I move an article from a group to another, this expiry does not
  happen, and so old data is kept into the agent. If I later come back
  into that "source" group, I see the old article (marked with G), and I
  can not remove it anymore. So, I currently have to copy the article in
  the destination group, then delete it, to keep the agent up to date.
  Even using "gnus-agent-regenerate" does not always clean up the
  situation.

I am having a problem that I think is the same one.  I use imap for
mail.  I have a function to make imap sharing with tbird etc. easier:

  d runs the command gdt-gnus-move-to-trash
    which is an interactive Lisp function in `/usr/home/gdt/.dot-gdt/.emacs'.
  It is bound to d.
  (gdt-gnus-move-to-trash)

(defun gdt-gnus-move-to-trash ()
  (interactive)
  (gnus-summary-move-article nil gdt-trash-newsgroup))


and have been noticing G articles in the summary on reentry.  I fix this
by "rm -rf News/agent".  This behavior started about 2 months ago (by
very fuzzy memory).