Emacs version: 25.0.91.1
OS: Debian 8 GNU/Linux
When I create a symlink in my ~/.emacs.d directory to my init.el file at some other location, and the init file does not have "(package-initialize)" inside it, then when package.el adds the "(package-initialize)" line to my init file on startup, instead of updating the original file, it seems to make a copy of the symlinked file in the ~/.emacs.d directory. This is bad, because now (probably without my immediate knowledge), I now have two very similar init files, and editing the supposedly-symlinked one will do nothing.
I don't really like the idea of my init file being written-to without my consent in the first place. But anyway, Emacs should at least do me the courtesy of modifying the symlinked file, because that's clearly the only copy of the file I want to maintain.