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From: Richard Stallman <rms@gnu.org>
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Subject: Re: site-start.el and subdirs.el
Date: Thu, 10 Apr 2003 02:22:41 -0400
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    In startup.el, normal-top-level loads any subdirs.el files found in
    load-path. Later on, it calls command-line which loads site-start.el
    and default.el. This means that if these two files (or ~/.emacs) add
    any directories to load-path, they don't get scanned for subdirs.el
    files.

The subdirs files are generated by Emacs makefiles, and they generate
these files only in certain directories.  Those are the directories
where Emacs checks for subdirs files.

I see no reason to support hand-edited subdirs.el files in other
directories.  You may as well list the subdirs by hand in .emacs as
list them by hand in subdirs.el.