Refactor doom-initialize-packages & package API

- Packages are initialized once, when package.el is first loaded, and
  must be updated manually via doom/reload-packages.
- Package->module association is now stored in the package's PLIST under
  :modules. This is an internal property and cannot be explicitly set
  through `package!'
- Add doom-package-list function
- Rename doom-get-packages to doom-find-packages
- Updated doom-find-packages' docstring
- Added the :core filter to doom-find-packages
- Simplified doom-initialize-packages
- doom/reload calls doom/reload-packages if necessary.
- Fix redundant properties in doom-packages
- Remove tracking of after!, def-package! and def-package-hook! blocks.
  Replaced with doom-package-list being able to see all packages, even
  in disabled modules.
- Add :built-in property to package! for dummy packages. This is
  important so that doom/describe-package can see built-in packages.

core/cli/autoloads.el

@@ -318,7 +318,7 @@ modified."
   (prin1 `(setq load-path ',load-path
                 auto-mode-alist ',auto-mode-alist
                 Info-directory-list ',Info-directory-list
-                doom-disabled-packages ',doom-disabled-packages
+                doom-disabled-packages ',(mapcar #'car (doom-find-packages :disabled t))
                 package-activated-list ',package-activated-list)
          (current-buffer)))
 
@@ -352,10 +352,10 @@ This should be run whenever your `doom!' block or update your packages."
       (with-temp-file doom-package-autoload-file
         (doom--generate-header 'doom-reload-package-autoloads)
         (save-excursion
-          ;; Cache the important and expensive-to-initialize state here.
+          ;; Cache important and expensive-to-initialize state here.
           (doom--generate-var-cache)
           (print! (green "✓ Cached package state"))
-          ;; Loop through packages and concatenate all their autoloads files.
+          ;; Concatenate the autoloads of all installed packages.
           (doom--generate-package-autoloads)
           (print! (green "✓ Package autoloads included")))
         ;; Remove `load-path' and `auto-mode-alist' modifications (most of them,