Avoid changing value of defcustom package-enable-at-startup

Avoid changing value of defcustom package-enable-at-startup

* lisp/emacs-lisp/package.el (package--activated): New variable to
avoid changing value of defcustom 'package-enable-at-startup'.
(package-initialize): Don't set 'package-enable-at-startup'.
(package-initialize, package-activate-all): Set 'package--activated'
instead of 'package-enable-at-startup'.
(package--initialized): Add doc string.

* lisp/startup.el (command-line): Check if 'package--activated' is
non-nil before activating packages.

* doc/lispref/package.texi (Packaging Basics): Update docs.