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From: Jesper Harder <harder@myrealbox.com>
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Subject: Re: auto-saving in other directory
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"leo" <halloleo@noospaam.myrealbox.com> writes:

> for backup files (like "filename.~1~) i can easily tell emacs to
> create them in its own subdirectory via backup-directory-alist.
>
> regarding auto-saving files (like "#filename#") this mechanism
> doesn't exist.

I think you should be able to do it by customizing
`auto-save-file-name-transforms'.