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From: Richard Stallman <rms@gnu.org>
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Subject: Re: Should lisp/Makefile.in custom-deps be using EMACS or emacs?
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      Isn't ./src/emacs the binary that's eventually
    installed in bindir?

Yes.

			  If so, then isn't it *supposed* to be using the
    installed Lisp directories (unless it's overridden by EMACSLOADPATH or
    similar)?

When you run it uninstalled, it computes the load-path differently.
It should not contain the installed Emacs lisp directories.