Don't disable the warning. It's there for a good reason: ~/.emacs.d
shouldn't be in your load-path
.
This is because Emacs writes files to this directory, and therefore it's possible (there are existing cases) for those files to conflict with the names of elisp libraries. If you have this directory in your load path, and you have such a name clash, then Emacs will attempt to load the wrong file if that library is required.
Just change your configuration. It's trivial to move the elisp libraries you've placed in that directory into a sub-directory, and then update the code which was adding ~/.emacs.d
to your load-path, so that it adds the new sub-directory instead:
(add-to-list 'load-path (expand-file-name "~/.emacs.d/lisp"))
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