diff --git a/core/cli/packages.el b/core/cli/packages.el
index 931a2da5d..8733d5dc7 100644
--- a/core/cli/packages.el
+++ b/core/cli/packages.el
@@ -74,9 +74,7 @@ declaration) or dependency thereof that hasn't already been."
            (package local-repo)
          (let ((existed-p (file-directory-p (straight--repos-dir package))))
            (condition-case-unless-debug e
-               (and (straight-use-package
-                     (intern package) nil nil
-                     (make-string (1- (or doom-format-indent 1)) 32))
+               (and (straight-use-package (intern package))
                     (not existed-p)
                     (file-directory-p (straight--repos-dir package))
                     (if-let (commit (cdr (assoc package versions-alist)))
@@ -103,29 +101,23 @@ declaration) or dependency thereof that hasn't already been."
   (print! (start "(Re)building %spackages...") (if force-p "all " ""))
   (straight--transaction-finalize)
   (print-group!
-   (let ((straight-check-for-modifications
-          (when (file-directory-p (straight--modified-dir))
-            '(find-when-checking)))
-         (straight--allow-find (and straight-check-for-modifications t))
-         (straight--packages-not-to-rebuild
-          (or straight--packages-not-to-rebuild (make-hash-table :test #'equal)))
-         (straight-use-package-pre-build-functions
-          straight-use-package-pre-build-functions)
-         (n 0))
-     (add-hook! 'straight-use-package-pre-build-functions (cl-incf n))
-     (if force-p
-         (let ((straight--packages-to-rebuild :all))
-           (dolist (package (hash-table-keys straight--recipe-cache))
-             (straight-use-package
-              (intern package) nil nil
-              (make-string (1- (or doom-format-indent 1)) 32))))
-       (straight--make-package-modifications-available)
-       (dolist (recipe (hash-table-values straight--recipe-cache))
-         (straight--with-plist recipe (package local-repo no-build)
-           (unless (or no-build (null local-repo))
-             (straight-use-package
-              (intern package) nil nil
-              (make-string (or doom-format-indent 0) 32))))))
+   (let* ((n 0)
+          (straight-check-for-modifications
+           (when (file-directory-p (straight--modified-dir))
+             '(find-when-checking)))
+          (straight--allow-find (and straight-check-for-modifications t))
+          (straight--packages-not-to-rebuild
+           (or straight--packages-not-to-rebuild (make-hash-table :test #'equal)))
+          (straight--packages-to-rebuild
+           (or (if force-p :all straight--packages-to-rebuild)
+               (make-hash-table :test #'equal)))
+          (straight-use-package-pre-build-functions
+           (cons (lambda (&rest _) (cl-incf n))
+                 straight-use-package-pre-build-functions)))
+     (unless force-p
+       (straight--make-package-modifications-available))
+     (dolist (package (hash-table-keys straight--recipe-cache))
+       (straight-use-package (intern package)))
      (if (= n 0)
          (ignore (print! (success "No packages need rebuilding")))
        (print! (success "Rebuilt %d package(s)" n))
diff --git a/core/core-cli.el b/core/core-cli.el
index 23304d01b..3d483faae 100644
--- a/core/core-cli.el
+++ b/core/core-cli.el
@@ -239,9 +239,18 @@ It will ensure that unneeded packages are removed, all needed packages are
 installed, autoloads files are up-to-date and no byte-compiled files have gone
 stale."
     :bare t
-    (print! (start "Initiating a refresh of Doom Emacs..."))
-    (print-group!
-     (let (success)
+    (let (success)
+      ;; Ensures that no pre-existing state pollutes the generation of the new
+      ;; autoloads files.
+      (dolist (file (list doom-autoload-file doom-package-autoload-file))
+        (delete-file file)
+        (delete-file (byte-compile-dest-file file)))
+
+      (doom-initialize 'force 'noerror)
+      (doom-initialize-modules)
+
+      (print! (start "Synchronizing your config with Doom Emacs..."))
+      (print-group!
        (when (and (not inhibit-envvar-p)
                   (file-exists-p doom-env-file))
          (doom-cli-reload-env-file 'force))
diff --git a/core/core-packages.el b/core/core-packages.el
index 0a0a28e45..b6cdf3105 100644
--- a/core/core-packages.el
+++ b/core/core-packages.el
@@ -182,6 +182,19 @@ missing) and shouldn't be deleted.")
            (print! (warn "%s is not a valid answer, try again.") answer))
          (funcall fn))))))
 
+(defadvice! doom--straight-respect-print-indent-a (args)
+  :filter-args #'straight-use-package
+  (cl-destructuring-bind
+      (melpa-style-recipe &optional no-clone no-build cause interactive)
+      args
+    (list melpa-style-recipe no-clone no-build
+          (if (and (not cause)
+                   (boundp 'doom-format-indent)
+                   (> doom-format-indent 0))
+              (make-string (1- (or doom-format-indent 1)) 32)
+            cause)
+          interactive)))
+
 
 ;;
 ;;; Bootstrapper