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From: Glenn Morris <rgm@gnu.org>
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Subject: Re: Getting rid of the GUI pop-ups
Date: Wed, 15 Feb 2017 21:14:39 -0500
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To: torys.anderson@gmail.com (Tory S. Anderson)
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Tory S. Anderson wrote:

> With Emacs 25.1.1, password prompts are no longer in the menu bar but
> via my (KDE/Plasma) window manager.
[...]
> I see these prompts most often when opening .gpg files and when trying
> to perform a git push.

I think you'll find these are gpg dialogue boxes, not Emacs ones. See eg

http://lists.gnu.org/archive/html/help-gnu-emacs/2016-02/msg00102.html
http://stackoverflow.com/questions/16826849/emacs-stop-popup-window-for-gpg-passphrase