--- footnote.el	2017-12-17 18:40:22.940312994 -0500
+++ footnote.el_new	2017-12-17 19:00:27.713722813 -0500
@@ -131,6 +131,14 @@ has no effect on buffers already display
   :type 'regexp
   :group 'footnote)
 
+(defcustom Footnote-align-to-fn-text t
+"Nil if footnote text is to be aligned flush left with left side
+of the footnote number. Non-nil if footnote text is to be aligned
+left with the first character of footnote text."
+  :type  'boolean
+  :group 'footnote)
+(make-variable-buffer-local 'Footnote-align-to-fn-text)
+
 ;;; Private variables
 
 (defvar footnote-style-number nil
@@ -148,6 +156,12 @@ has no effect on buffers already display
 (defvar footnote-mouse-highlight 'highlight
   "Text property name to enable mouse over highlight.")
 
+(defvar Footnote--body-auto-fill-prefix nil
+"When Footnmote mode modifies variable `fill-prefix', store the
+prior value here, so that it can be restored when leaving the
+footnote area.")
+(make-variable-buffer-local 'Footnote--body-auto-fill-prefix)
+
 ;;; Default styles
 ;;; NUMERIC
 (defconst footnote-numeric-regexp "[0-9]+"
@@ -609,8 +623,72 @@ Return nil if the cursor is not over a f
   (or (get-text-property (point) 'footnote-number)
       (Footnote-text-under-cursor)))
 
+(defun Footnote--calc-fn-alignment-column()
+"Calculate the left alignment for footnote text."
+  (+ footnote-body-tag-spacing
+    (length
+       (concat footnote-start-tag  footnote-end-tag
+         (Footnote-index-to-string
+            (caar (last footnote-text-marker-alist)))))))
+
+(defun Footnote--align-to-body()
+  (when (not Footnote-align-to-fn-text)
+    (setq fill-prefix Footnote--body-auto-fill-prefix)
+    (setq Footnote--body-auto-fill-prefix nil)))
+
+(defun Footnote--point-in-body-p()
+  "Return `t' if point is in the buffer text area, ie. before the beginning of
+the footnote area."
+  ; NOTE: This code is shared with a patch I've proposed for emacs-bug#29756
+  (let
+    ((p (point))
+     (q (if (not footnote-text-marker-alist) (point-max)
+         (if (string-equal footnote-section-tag "")
+           (cdr (first footnote-text-marker-alist))
+          (goto-char (cdr (first footnote-text-marker-alist)))
+          (if (re-search-backward
+                (concat "^" footnote-section-tag-regexp) nil t)
+            (match-beginning 0)
+           ; This `else' should never happen, and indicates an error, ie. footnotes
+           ; already exist and a footnote-section-tag is defined, but the section tag
+           ; hasn't been found. We choose to assume that the user deleted it
+           ; intentionally and wants us to behave in this buffer as if the section tag
+           ; was set "", so we do that, now.
+           (setq footnote-section-tag "")
+           ; HOWEVER: The rest of footnote mode does not currently honor or account
+           ; for this.
+           ;
+           ; To illustrate the difference in behavior, create a few footnotes, delete
+           ; the section tag, and create another footnote. Then undo, comment the
+           ; above line (that sets the tag to ""), re-evaluate this function, and repeat.
+           (cdr (first footnote-text-marker-alist))
+         )))))
+   (goto-char p) ; undo `re-search-backward' side-effect
+   (if (< p q) t nil)))
+
 ;;; User functions
 
+(defun Footnote-toggle-alignment()
+  "Change whether footnote text is aligned flush left with the
+left of a footnote's number, or flush left with the first
+character of footnote text on the footnote's first line."
+  (interactive)
+  (setq Footnote-align-to-fn-text (not Footnote-align-to-fn-text))
+  (when footnote-text-marker-alist
+    (if (>= (point) (cdr (first footnote-text-marker-alist)))
+      (if Footnote-align-to-fn-text
+        (Footnote--align-to-fn)
+       (Footnote--align-to-body))))
+  (if Footnote-align-to-fn-text
+    (message "Footnotes will left-align to footnote text")
+   (message "Footnotes will left-align to body text")))
+
+(defun Footnote-fill-paragraph(&optional justify region)
+  (when (and (Footnote--point-in-body-p) Footnote--body-auto-fill-prefix)
+    (setq fill-prefix Footnote--body-auto-fill-prefix)
+    (setq Footnote--body-auto-fill-prefix nil))
+  (fill-paragraph justify region))
+
 (defun Footnote-make-hole ()
   (save-excursion
     (let ((i 0)
@@ -661,7 +739,10 @@ by using `Footnote-back-to-message'."
 	  (Footnote-narrow-to-footnotes)))
       ;; Emacs/XEmacs bug?  save-excursion doesn't restore point when using
       ;; insert-before-markers.
-      (goto-char opoint))))
+      (goto-char opoint))
+    (when Footnote-align-to-fn-text
+      (setq Footnote--body-auto-fill-prefix (or fill-prefix ""))
+      (setq fill-prefix (make-string (Footnote--calc-fn-alignment-column) 32)))))
 
 (defun Footnote-delete-footnote (&optional arg)
   "Delete a numbered footnote.
@@ -767,7 +848,9 @@ being set it is automatically widened."
     (when note
       (when footnote-narrow-to-footnotes-when-editing
 	(widen))
-      (goto-char (cadr (assq note footnote-pointer-marker-alist))))))
+      (goto-char (cadr (assq note footnote-pointer-marker-alist)))
+   (setq fill-prefix Footnote--body-auto-fill-prefix)
+   (setq Footnote--body-auto-fill-prefix nil))))
 
 (defvar footnote-mode-map
   (let ((map (make-sparse-keymap)))
@@ -778,6 +861,8 @@ being set it is automatically widened."
     (define-key map "g" 'Footnote-goto-footnote)
     (define-key map "r" 'Footnote-renumber-footnotes)
     (define-key map "s" 'Footnote-set-style)
+    (define-key map (kbd "M-q") 'Footnote-toggle-alignment)
+    (define-key map [remap fill-paragraph] 'Footnote-fill-paragraph)
     map))
 
 (defvar footnote-minor-mode-map