I encountered a few problems with org-mac-mail bundled with emacs 24.3.1; some 
errors interfacing with Growl (2.1) so the patch below works for me and I 
wondered whether it would be of use to anyone else.

I adapted the insertion of flagged mail to look at all active mail accounts 
rather than having to name any particular one.

This is how I use org-mac-message: and below is the patch.

(require 'org)
(load "org-mac-message")
(global-set-key [(shift f10)] (lambda() (interactive)
                                (progn
                                  (find-file-noselect 
"~/Dropbox/org/refile.org")
                                  (org-mac-message-insert-flagged "refile.org" 
"Flagged mail"))))


diff --git a/org-mac-message.el b/org-mac-message.el
index 5df68f5..be2a654 100644
--- a/org-mac-message.el
+++ b/org-mac-message.el
@@ -95,86 +95,89 @@ This will use the command `open' with the message URL."
     "return theLinkList as string\n"
     "end tell")))
 
-(defun as-get-flagged-mail ()
-  "AppleScript to create links to flagged messages in Mail.app."
-  (do-applescript
-   (concat
-    ;; Is Growl installed?
-    "tell application \"System Events\"\n"
-    "set growlHelpers to the name of every process whose creator type contains 
\"GRRR\"\n"
-    "if (count of growlHelpers) > 0 then\n"
-    "set growlHelperApp to item 1 of growlHelpers\n"
-    "else\n"
-    "set growlHelperApp to \"\"\n"
-    "end if\n"
-    "end tell\n"
-
-    ;; Get links
-    "tell application \"Mail\"\n"
-    "set theMailboxes to every mailbox of account \"" org-mac-mail-account 
"\"\n"
-    "set theLinkList to {}\n"
-    "repeat with aMailbox in theMailboxes\n"
-    "set theSelection to (every message in aMailbox whose flagged status = 
true)\n"
-    "repeat with theMessage in theSelection\n"
-    "set theID to message id of theMessage\n"
-    "set theSubject to subject of theMessage\n"
-    "set theLink to \"message://\" & theID & \"::split::\" & theSubject & 
\"\n\"\n"
-    "copy theLink to end of theLinkList\n"
-
-    ;; Report progress through Growl
-    ;; This "double tell" idiom is described in detail at
-    ;; http://macscripter.net/viewtopic.php?id=24570 The
-    ;; script compiler needs static knowledge of the
-    ;; growlHelperApp.  Hmm, since we're compiling
-    ;; on-the-fly here, this is likely to be way less
-    ;; portable than I'd hoped.  It'll work when the name
-    ;; is still "GrowlHelperApp", though.
-    "if growlHelperApp is not \"\" then\n"
-    "tell application \"GrowlHelperApp\"\n"
-    "tell application growlHelperApp\n"
-    "set the allNotificationsList to {\"FlaggedMail\"}\n"
-    "set the enabledNotificationsList to allNotificationsList\n"
-    "register as application \"FlaggedMail\" all notifications 
allNotificationsList default notifications enabledNotificationsList icon of 
application \"Mail\"\n"
-    "notify with name \"FlaggedMail\" title \"Importing flagged message\" 
description theSubject application name \"FlaggedMail\"\n"
-    "end tell\n"
-    "end tell\n"
-    "end if\n"
-    "end repeat\n"
-    "end repeat\n"
-    "return theLinkList as string\n"
-    "end tell")))
+(defun  as-get-flagged-mail ()
+     "AppleScript to create links to flagged messages in all Mail.app accounts"
+     ;; Revised use of Growl interface and no need for variable 
org-mac-mail-account
+     (do-applescript
+      (concat
+       ;; Is Growl running? Use API as recommended at 
http://growl.info/documentation/applescript-support.php 
+       "tell application \"System Events\"\n"
+       "set growlIsRunning to (count of (every process whose bundle identifier 
is \"com.Growl.GrowlHelperApp\")) > 0\n"
+       "end tell\n"
+
+       "set theLinkList to {}\n"
+       "set isNotRegisteredToGrowl to true\n"
+       "tell application \"Mail\"\n"
+       "set theAccountList to the name of every account\n"
+       "repeat with theMailAccount in theAccountList\n"
+       "set theMailboxes to every mailbox of account theMailAccount\n"
+       "repeat with aMailbox in theMailboxes\n"
+       "set theSelection to (every message in aMailbox whose flagged status = 
true)\n"
+       "repeat with theMessage in theSelection\n"
+       "set theID to message id of theMessage\n"
+       "set theSubject to subject of theMessage\n"
+       "set theLink to \"message://\" & theID & \"::split::\" & theSubject & 
\"\n\"\n"
+       "copy theLink to end of theLinkList\n"
+       
+       "if growlIsRunning then\n"
+       "tell application id \"com.Growl.GrowlHelperApp\"\n"
+       "if isNotRegisteredToGrowl then\n"
+       "set the allNotificationsList to {\"FlaggedMail\"}\n"
+       "set the enabledNotificationsList to allNotificationsList\n"
+       "register as application \"FlaggedMail\" all notifications 
allNotificationsList default notifications enabledNotificationsList icon of 
application \"Mail\"\n"
+       "set isNotRegisteredToGrowl to false\n"
+       "end if\n"
+       "notify with name \"FlaggedMail\" title \"Importing flagged message\" 
description theSubject application name \"FlaggedMail\"\n"
+       "end tell\n"
+       "end if\n"
+       
+       "end repeat\n"
+       "end repeat\n"
+       "end repeat\n"
+       "end tell\n"
+       "return theLinkList as string\n"
+       ))
+     )
 
 (defun org-mac-message-get-links (&optional select-or-flag)
-  "Create links to the messages currently selected or flagged in Mail.app.
+     "Overridden function.
+Create links to the messages currently selected or flagged in Mail.app.
 This will use AppleScript to get the message-id and the subject of the
 messages in Mail.app and make a link out of it.
 When SELECT-OR-FLAG is \"s\", get the selected messages (this is also
 the default).  When SELECT-OR-FLAG is \"f\", get the flagged messages.
 The Org-syntax text will be pushed to the kill ring, and also returned."
-  (interactive "sLink to (s)elected or (f)lagged messages: ")
-  (setq select-or-flag (or select-or-flag "s"))
-  (message "AppleScript: searching mailboxes...")
-  (let* ((as-link-list
-         (if (string= select-or-flag "s")
-             (as-get-selected-mail)
-           (if (string= select-or-flag "f")
-               (as-get-flagged-mail)
-             (error "Please select \"s\" or \"f\""))))
-        (link-list
-         (mapcar
-          (lambda (x) (if (string-match "\\`\"\\(.*\\)\"\\'" x) (setq x 
(match-string 1 x))) x)
-          (split-string as-link-list "[\r\n]+")))
-        split-link URL description orglink orglink-insert rtn orglink-list)
-    (while link-list
-      (setq split-link (split-string (pop link-list) "::split::"))
-      (setq URL (car split-link))
-      (setq description (cadr split-link))
-      (when (not (string= URL ""))
-       (setq orglink (org-make-link-string URL description))
-       (push orglink orglink-list)))
-    (setq rtn (mapconcat 'identity orglink-list "\n"))
-    (kill-new rtn)
-    rtn))
+     (interactive "sLink to (s)elected or (f)lagged messages: ")
+     (setq select-or-flag (or select-or-flag "s"))
+     (let* ((as-link-list
+            (if (string= select-or-flag "s")
+                (progn
+                  (message "AppleScript: searching mailboxes for selected 
message")
+                  (as-get-selected-mail))
+              (if (string= select-or-flag "f")
+                  (progn      
+                    ;; searching for all flagged messages can take tens of 
seconds
+                    ;; so user needs to be told of progress even if Growl is 
also notifying 
+                    (message "AppleScript: searching mailboxes for flagged 
messages")
+                    (as-get-flagged-mail))
+                (error "Please select \"s\" or \"f\""))))
+           (link-list
+            (mapcar
+             (lambda (x) (if (string-match "\\`\"\\(.*\\)\"\\'" x) (setq x 
(match-string 1 x))) x)
+             (split-string as-link-list "[\r\n]+")))
+           split-link URL description orglink orglink-insert rtn orglink-list)
+       (while link-list
+        (setq split-link (split-string (pop link-list) "::split::"))
+        (setq URL (car split-link))
+        (setq description (cadr split-link))
+        (when (not (string= URL ""))
+          (setq orglink (org-make-link-string URL description))
+          (push orglink orglink-list)))
+       (setq rtn (mapconcat 'identity orglink-list "\n"))
+       (kill-new rtn)
+       ;; "searching" message will remain in echo area until replaced
+       (message "AppleScript: finished searching mailboxes.")
+       rtn))
 
 (defun org-mac-message-insert-selected ()
   "Insert a link to the messages currently selected in Mail.app.
@@ -186,30 +189,41 @@ active mail in Mail.app and make a link out of it."
 ;; The following line is for backward compatibility
 (defalias 'org-mac-message-insert-link 'org-mac-message-insert-selected)
 
-(defun org-mac-message-insert-flagged (org-buffer org-heading)
-  "Asks for an org buffer and a heading within it, and replace message links.
+(eval-after-load "org-mac-message"
+  '(defun org-mac-message-insert-flagged (org-buffer org-heading)
+     "Asks for an org buffer and a heading within it, and replace message 
links.
 If heading exists, delete all message:// links within heading's first
 level.  If heading doesn't exist, create it at point-max.  Insert
 list of message:// links to flagged mail after heading."
-  (interactive "bBuffer in which to insert links: \nsHeading after which to 
insert links: ")
-  (with-current-buffer org-buffer
-    (goto-char (point-min))
-    (let ((isearch-forward t)
-         (message-re 
"\\[\\[\\(message:\\)\\([^]]+\\)\\]\\(\\[\\([^]]+\\)\\]\\)?\\]"))
-      (if (org-goto-local-search-headings org-heading nil t)
-         (if (not (eobp))
-             (progn
-               (save-excursion
-                 (while (re-search-forward
-                         message-re (save-excursion (outline-next-heading)) t)
-                   (delete-region (match-beginning 0) (match-end 0)))
-                 (insert "\n" (org-mac-message-get-links "f")))
-               (flush-lines "^$" (point) (outline-next-heading)))
-           (insert "\n" (org-mac-message-get-links "f")))
-       (goto-char (point-max))
-       (insert "\n")
-       (org-insert-heading nil t)
-       (insert org-heading "\n" (org-mac-message-get-links "f"))))))
+     (interactive "bBuffer in which to insert links: \nsHeading after which to 
insert links: ")
+     (with-current-buffer org-buffer
+       (goto-char (point-min))
+       (let ((isearch-forward t)
+            (message-re 
"\\[\\[\\(message:\\)\\([^]]+\\)\\]\\(\\[\\([^]]+\\)\\]\\)?\\]"))
+        (if (org-goto-local-search-headings org-heading nil t)
+            (if (not (eobp))
+                (progn
+                  (save-excursion
+                    ;; delete previously recorded flagged messages
+                    (while (re-search-forward
+                            message-re (save-excursion (outline-next-heading)) 
t)
+                      (delete-region (match-beginning 0) (match-end 0)))
+                    (insert "\n" (org-mac-message-get-links "f")))
+                  ;; apparently also delete empty lines.
+                  ;; allow for situation where there is no next-heading
+                  ;; to avoid previously ocurring Lisp errors
+                  (let (
+                        (frm (point))
+                        (tom (outline-next-heading)))
+                    (if (null tom) (setq tom (point-max)))
+                    (flush-lines "^$" frm tom)))
+
+              (insert "\n" (org-mac-message-get-links "f")))
+          (goto-char (point-max))
+          (insert "\n")
+          (org-insert-heading nil t)
+          (insert org-heading "\n" (org-mac-message-get-links "f"))))))
+  )
 
 (provide 'org-mac-message)
 


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