notmuch.el: Indent messages to show nested structure of thread.

Now that we're actually adding text to the buffer for the indentation,
our old aproach of using positions to record regions to manipulate is
now longer correct. Fortunately, it's easy to switch from positions to
markers which are robust, (just call point-marker instead of point and
all relevant functions accept markers as well as points).

I also finally fixed the bug where the text "[6 line signature]" we
display was causing the one-line-summary of the next message to be on
its same line rather than at the beginning of the next line where it
belongs.

notmuch.el

@@ -57,7 +57,7 @@
   "Keymap for \"notmuch show\" buffers.")
 (fset 'notmuch-show-mode-map notmuch-show-mode-map)
 
-(defvar notmuch-show-signature-lines-max 6
+(defvar notmuch-show-signature-lines-max 12
   "Maximum length of signature that will be hidden by default.")
 
 (set 'notmuch-show-message-begin-regexp    "message{")
@@ -73,6 +73,7 @@
 (set 'notmuch-show-marker-regexp "\\(message\\|header\\|body\\|attachment\\|part\\)[{}].*$")
 
 (set 'notmuch-show-id-regexp "\\(id:[^ ]*\\)")
+(set 'notmuch-show-depth-regexp " depth:\\([0-9]*\\) ")
 (set 'notmuch-show-filename-regexp "filename:\\(.*\\)$")
 (set 'notmuch-show-tags-regexp "(\\([^)]*\\))$")
 
@@ -425,65 +426,98 @@ which this thread was originally shown."
 	(if last
 	    (notmuch-show-archive-thread))))))
 
-(defun notmuch-show-markup-citations-region (beg end)
+(defun notmuch-show-markup-citations-region (beg end depth)
   (goto-char beg)
   (beginning-of-line)
   (while (< (point) end)
-    (let ((beg-sub (point)))
-      (if (looking-at ">")
+    (let ((beg-sub (point-marker))
+	  (indent (make-string depth ? ))
+	  (citation "[[:space:]]*>"))
+      (if (looking-at citation)
 	  (progn
-	    (while (looking-at ">")
+	    (while (looking-at citation)
 	      (forward-line))
 	    (let ((overlay (make-overlay beg-sub (point))))
 	      (overlay-put overlay 'invisible 'notmuch-show-citation)
 	      (overlay-put overlay 'before-string
-			   (concat "[" (number-to-string (count-lines beg-sub (point)))
+			   (concat indent
+				   "[" (number-to-string (count-lines beg-sub (point)))
 				   "-line citation. Press 'c' to show.]\n")))))
-      (if (looking-at "--[ ]?$")
-	  (let ((sig-lines (count-lines beg-sub end)))
+      (if (looking-at "[[:space:]]*-- ?$")
+	  (let ((sig-lines (- (count-lines beg-sub end) 1)))
 	    (if (<= sig-lines notmuch-show-signature-lines-max)
 		(progn
-		  (overlay-put (make-overlay beg-sub (+ beg-sub 1))
-			       'before-string
-			       (concat "[" (number-to-string sig-lines)
-				       "-line signature. Press 's' to show.]"))
-		  (overlay-put (make-overlay (+ beg-sub 2) end)
+		  (overlay-put (make-overlay beg-sub end)
 			       'invisible 'notmuch-show-signature)
+		  (overlay-put (make-overlay beg (- beg-sub 1))
+			       'after-string
+			       (concat "\n" indent
+				       "[" (number-to-string sig-lines)
+				       "-line signature. Press 's' to show.]"))
 		  (goto-char end)))))
       (forward-line))))
 
-(defun notmuch-show-markup-body ()
+(defun notmuch-show-markup-part (beg end depth)
+  (if (re-search-forward notmuch-show-part-begin-regexp nil t)
+      (progn
+	(forward-line)
+	(let ((beg (point-marker)))
+	  (re-search-forward notmuch-show-part-end-regexp)
+	  (let ((end (copy-marker (match-beginning 0))))
+	    (indent-rigidly beg end depth)
+	    (notmuch-show-markup-citations-region beg end depth)
+	    ; Advance to the next part (if any) (so the outer loop can
+	    ; determine whether we've left the current message.
+	    (re-search-forward notmuch-show-part-begin-regexp nil t))))
+    (goto-char end)))
+
+(defun notmuch-show-markup-parts-region (beg end depth)
+  (save-excursion
+    (goto-char beg)
+    (while (< (point) end)
+      (notmuch-show-markup-part beg end depth))))
+
+(defun notmuch-show-markup-body (depth)
   (re-search-forward notmuch-show-body-begin-regexp)
-  (next-line 1)
-  (beginning-of-line)
-  (let ((beg (point)))
+  (forward-line)
+  (let ((beg (point-marker)))
     (re-search-forward notmuch-show-body-end-regexp)
-    (let ((end (match-beginning 0)))
-      (notmuch-show-markup-citations-region beg end)
+    (let ((end (copy-marker (match-beginning 0))))
+      (notmuch-show-markup-parts-region beg end depth)
       (if (not (notmuch-show-message-unread-p))
 	  (overlay-put (make-overlay beg end)
-		       'invisible 'notmuch-show-body-read)))))
+		       'invisible 'notmuch-show-body-read))
+      (set-marker beg nil)
+      (set-marker end nil)
+      )))
 
-(defun notmuch-show-markup-header ()
+(defun notmuch-show-markup-header (depth)
   (re-search-forward notmuch-show-header-begin-regexp)
-  (forward-line 1)
-  (beginning-of-line)
-  (let ((beg (point)))
+  (forward-line)
+  (let ((beg (point-marker)))
     (end-of-line)
     ; Inverse video for subject
     (overlay-put (make-overlay beg (point)) 'face '((cons :inverse-video t)))
-    (beginning-of-line)
     (forward-line 2)
-    (set 'beg (point))
+    (let ((beg-hidden (point-marker)))
       (re-search-forward notmuch-show-header-end-regexp)
-    (overlay-put (make-overlay beg (match-beginning 0))
-		 'invisible 'notmuch-show-header)))
+      (beginning-of-line)
+      (let ((end (point-marker)))
+	(indent-rigidly beg end depth)
+	(overlay-put (make-overlay beg-hidden end)
+		     'invisible 'notmuch-show-header)
+	(set-marker beg nil)
+	(set-marker beg-hidden nil)
+	(set-marker end nil)
+	))))
 
 (defun notmuch-show-markup-message ()
   (if (re-search-forward notmuch-show-message-begin-regexp nil t)
       (progn
-	(notmuch-show-markup-header)
-	(notmuch-show-markup-body))
+	(re-search-forward notmuch-show-depth-regexp)
+	(let ((depth (string-to-number (buffer-substring (match-beginning 1) (match-end 1)))))
+	  (notmuch-show-markup-header depth)
+	  (notmuch-show-markup-body depth)))
     (goto-char (point-max))))
 
 (defun notmuch-show-hide-markers ()