In my `init.el`, I have the following line

```lisp
(setq custom-file (expand-file-name "custom.el" user-emacs-directory))
```

which is supposed to set the file `custom.el` into `.emacs.d` config folder for getting all customization tidy.
 
Over the years, emacs populated this file with various things. I just ran customization with `M-x customize-variable` and discovered that emacs added the new custom into `custom.el`, overwriting the previous version of the file.

What's the mistake?