New bin/doom (eventual replacement for make)

This commit adds bin/doom, which acts as the middle man that make once
was (and will stay for a while, though the documentation will shift away
from using it). It does everything the previous make interface did, but
is faster and more flexible. bin/doom should eventually replace the
makefile.

bin/doom also makes it easier to run Doom outside of ~/.emacs.d and
~/.doom.d with, for example:

  bin/doom run -p ~/.other.doom.d/ -e ~/.other.emacs.d

bin/doom.cmd is included for Windows users, but I don't recommend using
it yet. It hasn't been tested nor have I ever written a batch script
before.

Also update init.example.el with new defaults.

core/autoload/modules.el

@@ -59,7 +59,6 @@ This should be run whenever init.el or an autoload file is modified. Running
         (generate-autoload-section-trailer "")
         (doom--stage 'autoloads)
         outdated)
-    (doom-initialize)
     (dolist (path (doom-module-load-path))
       (let ((auto-dir  (expand-file-name "autoload" path))
             (auto-file (expand-file-name "autoload.el" path)))