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From: Richard Stallman <rms@gnu.org>
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Subject: Re: paths
Date: Sat, 22 Feb 2003 03:15:34 -0500
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    I suspect this was because of name conflicts with code loaded from
    /usr/local/share/emacs/site-lisp
    which existed prior to the installation of the updated version.

Emacs obeyed your customizations.

    In src/epaths.h, changing the ordering of directories in the path:

    define PATH_LOADSEARCH "/usr/local/share/emacs/21.2/site-lisp:/usr/local/share/emacs/site-lisp:/usr/local/share/emacs/21.2/leim:/usr/local/share/emacs/21.2/lisp"

It is a feature that your locally installed packages override the
standard ones.  If you want them to apply to just a single Emacs
version, put them in the directory that includes the Emacs version
number.

Basically, you got what you asked for, so if that isn't what you
really want, you should ask for what you really want.