When I configure variable through M-x customize-variable, emacs save it to .emacs instead .emacs.d/init.el. On Windows I have no this problem, it uses init.el by default. But on Linux it creates me .emacs file. How to make emacs force use .emacs.d/init.el ?
~/.emacs
file to ~/.emacs.d/init.el
See https://www.gnu.org/software/emacs/manual/html_node/emacs/Find-Init.html for details.