Small enhancements to the main Org menu.

* org.el (org-in-subtree-not-table-p): New utility function
for building the menu.
(org-org-menu): Add an item for refiling.  Check more contexts
when activating items.
(org-tree-to-indirect-buffer): Use `org-up-heading-safe'.

* org-agenda.el (org-agenda-tree-to-indirect-buffer)
(org-agenda-do-tree-to-indirect-buffer): Use argument `arg'.

lisp/org-agenda.el

@@ -2200,7 +2200,7 @@ The following commands are available:
     ["Capture with cursor date" org-agenda-capture t]
     ["Follow Mode" org-agenda-follow-mode
      :style toggle :selected org-agenda-follow-mode :active t]
-					;    ["Tree to indirect frame" org-agenda-tree-to-indirect-buffer t]
+    ;;    ["Tree to indirect frame" org-agenda-tree-to-indirect-buffer t]
     "--"
     ("TODO"
      ["Cycle TODO" org-agenda-todo t]
@@ -7480,7 +7480,7 @@ When called with a prefix argument, include all archive files as well."
     (when (and (markerp m) (marker-buffer m))
       (and org-agenda-follow-mode
 	   (if org-agenda-follow-indirect
-	       (org-agenda-tree-to-indirect-buffer)
+	       (org-agenda-tree-to-indirect-buffer nil)
 	     (org-agenda-show)))
       (and org-agenda-show-outline-path
 	   (org-with-point-at m (org-display-outline-path t))))))
@@ -7865,22 +7865,23 @@ docstring of `org-agenda-show-1'."
 (defun org-agenda-error ()
   (error "Command not allowed in this line"))
 
-(defun org-agenda-tree-to-indirect-buffer ()
+(defun org-agenda-tree-to-indirect-buffer (arg)
   "Show the subtree corresponding to the current entry in an indirect buffer.
-This calls the command `org-tree-to-indirect-buffer' from the original
-Org-mode buffer.
-With numerical prefix arg ARG, go up to this level and then take that tree.
+This calls the command `org-tree-to-indirect-buffer' from the original buffer.
+
+With a numerical prefix ARG, go up to this level and then take that tree.
+With a negative numeric ARG, go up by this number of levels.
 With a \\[universal-argument] prefix, make a separate frame for this tree (i.e. don't
 use the dedicated frame)."
-  (interactive)
-  (if (and current-prefix-arg (listp current-prefix-arg))
-      (org-agenda-do-tree-to-indirect-buffer)
+  (interactive "P")
+  (if current-prefix-arg
+      (org-agenda-do-tree-to-indirect-buffer arg)
     (let ((agenda-buffer (buffer-name))
 	  (agenda-window (selected-window))
           (indirect-window
 	   (and org-last-indirect-buffer
 		(get-buffer-window org-last-indirect-buffer))))
-      (save-window-excursion (org-agenda-do-tree-to-indirect-buffer))
+      (save-window-excursion (org-agenda-do-tree-to-indirect-buffer arg))
       (unless (or (eq org-indirect-buffer-display 'new-frame)
 		  (eq org-indirect-buffer-display 'dedicated-frame))
 	(unwind-protect
@@ -7892,7 +7893,7 @@ use the dedicated frame)."
 	  (fit-window-to-buffer indirect-window)))
       (select-window (get-buffer-window agenda-buffer)))))
 
-(defun org-agenda-do-tree-to-indirect-buffer ()
+(defun org-agenda-do-tree-to-indirect-buffer (arg)
   "Same as `org-agenda-tree-to-indirect-buffer' without saving window."
   (org-agenda-check-no-diary)
   (let* ((marker (or (org-get-at-bol 'org-marker)
@@ -7902,7 +7903,7 @@ use the dedicated frame)."
     (with-current-buffer buffer
       (save-excursion
 	(goto-char pos)
-	(call-interactively 'org-tree-to-indirect-buffer)))))
+	(funcall 'org-tree-to-indirect-buffer arg)))))
 
 (defvar org-last-heading-marker (make-marker)
   "Marker pointing to the headline that last changed its TODO state

lisp/org.el

@@ -7092,8 +7092,9 @@ or nil."
 
 (defun org-tree-to-indirect-buffer (&optional arg)
   "Create indirect buffer and narrow it to current subtree.
-With numerical prefix ARG, go up to this level and then take that tree.
+With a numerical prefix ARG, go up to this level and then take that tree.
 If ARG is negative, go up that many levels.
+
 If `org-indirect-buffer-display' is not `new-frame', the command removes the
 indirect buffer previously made with this command, to avoid proliferation of
 indirect buffers.  However, when you call the command with a \
@@ -7115,7 +7116,7 @@ frame is not changed."
 	(setq level (org-outline-level))
 	(if (< arg 0) (setq arg (+ level arg)))
 	(while (> (setq level (org-outline-level)) arg)
-	  (outline-up-heading 1 t)))
+	  (org-up-heading-safe)))
       (setq beg (point)
 	    heading (org-get-heading))
       (org-end-of-subtree t t)
@@ -19584,6 +19585,11 @@ See the individual commands for more information."
 
 ;;; Menu entries
 
+(defsubst org-in-subtree-not-table-p ()
+  "Are we in a subtree and not in a table?"
+  (and (not (org-before-first-heading-p))
+       (not (org-at-table-p))))
+
 ;; Define the Org-mode menus
 (easy-menu-define org-tbl-menu org-mode-map "Tbl menu"
   '("Tbl"
@@ -19666,23 +19672,25 @@ See the individual commands for more information."
      "--"
      ["Jump" org-goto t])
     ("Edit Structure"
-     ["Move Subtree Up" org-shiftmetaup (not (org-at-table-p))]
-     ["Move Subtree Down" org-shiftmetadown (not (org-at-table-p))]
+     ["Refile Subtree" org-refile (org-in-subtree-not-table-p)]
      "--"
-     ["Copy Subtree"  org-copy-special (not (org-at-table-p))]
-     ["Cut Subtree"  org-cut-special (not (org-at-table-p))]
+     ["Move Subtree Up" org-shiftmetaup (org-in-subtree-not-table-p)]
+     ["Move Subtree Down" org-shiftmetadown (org-in-subtree-not-table-p)]
+     "--"
+     ["Copy Subtree"  org-copy-special (org-in-subtree-not-table-p)]
+     ["Cut Subtree"  org-cut-special (org-in-subtree-not-table-p)]
      ["Paste Subtree"  org-paste-special (not (org-at-table-p))]
      "--"
      ["Clone subtree, shift time" org-clone-subtree-with-time-shift t]
      "--"
      ["Copy visible text"  org-copy-visible t]
      "--"
-     ["Promote Heading" org-metaleft (not (org-at-table-p))]
-     ["Promote Subtree" org-shiftmetaleft (not (org-at-table-p))]
-     ["Demote Heading"  org-metaright (not (org-at-table-p))]
-     ["Demote Subtree"  org-shiftmetaright (not (org-at-table-p))]
+     ["Promote Heading" org-metaleft (org-in-subtree-not-table-p)]
+     ["Promote Subtree" org-shiftmetaleft (org-in-subtree-not-table-p)]
+     ["Demote Heading"  org-metaright (org-in-subtree-not-table-p)]
+     ["Demote Subtree"  org-shiftmetaright (org-in-subtree-not-table-p)]
      "--"
-     ["Sort Region/Children" org-sort  (not (org-at-table-p))]
+     ["Sort Region/Children" org-sort t]
      "--"
      ["Convert to odd levels" org-convert-to-odd-levels t]
      ["Convert to odd/even levels" org-convert-to-oddeven-levels t])
@@ -19693,11 +19701,11 @@ See the individual commands for more information."
      ["Footnote new/jump" org-footnote-action t]
      ["Footnote extra" (org-footnote-action t) :active t :keys "C-u C-c C-x f"])
     ("Archive"
-     ["Archive (default method)" org-archive-subtree-default t]
+     ["Archive (default method)" org-archive-subtree-default (org-in-subtree-not-table-p)]
      "--"
-     ["Move Subtree to Archive file" org-advertized-archive-subtree t]
-     ["Toggle ARCHIVE tag" org-toggle-archive-tag t]
-     ["Move subtree to Archive sibling" org-archive-to-archive-sibling t]
+     ["Move Subtree to Archive file" org-advertized-archive-subtree (org-in-subtree-not-table-p)]
+     ["Toggle ARCHIVE tag" org-toggle-archive-tag (org-in-subtree-not-table-p)]
+     ["Move subtree to Archive sibling" org-archive-to-archive-sibling (org-in-subtree-not-table-p)]
      )
     "--"
     ("Hyperlinks"
@@ -19748,23 +19756,23 @@ See the individual commands for more information."
      ["Go to the inbox of a feed..." org-feed-goto-inbox t]
      ["Customize feeds" (customize-variable 'org-feed-alist) t])
     ("TAGS and Properties"
-     ["Set Tags" org-set-tags-command t]
+     ["Set Tags" org-set-tags-command (not (org-before-first-heading-p))]
      ["Change tag in region" org-change-tag-in-region (org-region-active-p)]
      "--"
-     ["Set property" org-set-property t]
+     ["Set property" org-set-property (not (org-before-first-heading-p))]
      ["Column view of properties" org-columns t]
      ["Insert Column View DBlock" org-insert-columns-dblock t])
     ("Dates and Scheduling"
-     ["Timestamp" org-time-stamp t]
-     ["Timestamp (inactive)" org-time-stamp-inactive t]
+     ["Timestamp" org-time-stamp (not (org-before-first-heading-p))]
+     ["Timestamp (inactive)" org-time-stamp-inactive (not (org-before-first-heading-p))]
      ("Change Date"
-      ["1 Day Later" org-shiftright t]
-      ["1 Day Earlier" org-shiftleft t]
-      ["1 ... Later" org-shiftup t]
-      ["1 ... Earlier" org-shiftdown t])
+      ["1 Day Later" org-shiftright (org-at-timestamp-p)]
+      ["1 Day Earlier" org-shiftleft (org-at-timestamp-p)]
+      ["1 ... Later" org-shiftup (org-at-timestamp-p)]
+      ["1 ... Earlier" org-shiftdown (org-at-timestamp-p)])
      ["Compute Time Range" org-evaluate-time-range t]
-     ["Schedule Item" org-schedule t]
-     ["Deadline" org-deadline t]
+     ["Schedule Item" org-schedule (not (org-before-first-heading-p))]
+     ["Deadline" org-deadline (not (org-before-first-heading-p))]
      "--"
      ["Custom time format" org-toggle-time-stamp-overlays
       :style radio :selected org-display-custom-times]