So, instead to have:
~/.emacs
~/.emacs.desktop
~/.emacs.desktop.lock
...
we could have:
~/.emacs.d/.emacs
~/.emacs.d/.emacs.desktop
~/.emacs.d/.emacs.desktop.lock
~/.emacs.d/mail
...
In this way we could have a more clean HOME!!!
That's the intention. Currently the strategy is to keep using the old
name if the file already exists, and to use the new name otherwise.
The strategy is not completely consistent in how to do it, because most
files in ~/.emacs.d are files which in $HOME should be hidden, but in
~/.emacs.d they don't have any reason to be hidden any more (nor to
include "emacs" in their name), so often the file in ~/.emacs.d doesn't
have the same name as in ~. In the case of desktop.el, OTOH you can
indeed move ~/.emacs.desktop to ~/.emacs.d.