diff --git a/lisp/ob-plantuml.el b/lisp/ob-plantuml.el
index c5045de6d..cb5ca129b 100644
--- a/lisp/ob-plantuml.el
+++ b/lisp/ob-plantuml.el
@@ -57,12 +57,14 @@ This function is called by `org-babel-execute-src-block'."
 	 (out-file (cdr (assoc :file params)))
 	 (cmdline (cdr (assoc :cmdline params)))
 	 (in-file (org-babel-temp-file "plantuml-"))
-	 (cmd (concat "java -jar "
-		      (shell-quote-argument org-plantuml-jar-path)
-		      " -p " cmdline " < "
-		      (shell-quote-argument in-file)
-		      " > "
-		      (shell-quote-argument out-file))))
+	 (cmd (if (not org-plantuml-jar-path)
+		  (error "`org-plantuml-jar-path' is not set")
+		(concat "java -jar "
+			(shell-quote-argument org-plantuml-jar-path)
+			" -p " cmdline " < "
+			(shell-quote-argument in-file)
+			" > "
+			(shell-quote-argument out-file)))))
     (unless (file-exists-p org-plantuml-jar-path)
       (error "Could not find plantuml.jar at %s" org-plantuml-jar-path))
     (with-temp-file in-file (insert (concat "@startuml\n" body "\n@enduml")))
diff --git a/lisp/ob-ruby.el b/lisp/ob-ruby.el
index f2363df33..87df8d10a 100644
--- a/lisp/ob-ruby.el
+++ b/lisp/ob-ruby.el
@@ -54,7 +54,6 @@
 
 (defun org-babel-expand-body:ruby (body params &optional processed-params)
   "Expand BODY according to PARAMS, return the expanded body."
-  (require 'inf-ruby)
   (let ((vars (nth 1 (or processed-params (org-babel-process-params params)))))
     (concat
      (mapconcat ;; define any variables
diff --git a/lisp/org-agenda.el b/lisp/org-agenda.el
index 90c693536..3a6434475 100644
--- a/lisp/org-agenda.el
+++ b/lisp/org-agenda.el
@@ -4002,8 +4002,7 @@ The remainder is either a list of TODO keywords, or a state symbol
   "Create agenda view for projects that are stuck.
 Stuck projects are project that have no next actions.  For the definitions
 of what a project is and how to check if it stuck, customize the variable
-`org-stuck-projects'.
-MATCH is being ignored."
+`org-stuck-projects'."
   (interactive)
   (let* ((org-agenda-skip-function
 	  'org-agenda-skip-entry-when-regexp-matches-in-subtree)
@@ -5118,7 +5117,7 @@ The modified list may contain inherited tags, and tags matched by
 	  (throw 'exit list))
       (while (setq time (pop gridtimes))
 	(unless (and remove (member time have))
-	  (setq time (format "%2d" time))
+	  (setq time (format "%4d" time))
 	  (push (org-format-agenda-item
 		 nil string "" nil
 		 (concat (substring time 0 -2) ":" (substring time -2)))
diff --git a/lisp/org-clock.el b/lisp/org-clock.el
index a0757c753..3328609fe 100644
--- a/lisp/org-clock.el
+++ b/lisp/org-clock.el
@@ -557,6 +557,13 @@ use libnotify if available, or fall back on a message."
 	((stringp org-show-notification-handler)
 	 (start-process "emacs-timer-notification" nil
 			org-show-notification-handler notification))
+	((featurep 'notifications)
+	 (notifications-notify
+	  :title "Org-mode message"
+	  :body notification
+	  ;; FIXME how to link to the Org icon?
+	  ;; :app-icon "~/.emacs.d/icons/mail.png"
+	  :urgency 'low))
 	((org-program-exists "notify-send")
 	 (start-process "emacs-timer-notification" nil
 			"notify-send" notification))
diff --git a/lisp/org-html.el b/lisp/org-html.el
index df55de02f..5da2a5fd1 100644
--- a/lisp/org-html.el
+++ b/lisp/org-html.el
@@ -720,7 +720,7 @@ MAY-INLINE-P allows inlining it as an image."
 			   ;;Substitute just if original path was absolute.
 			   ;;(Otherwise path must remain relative)
 			   (if (file-name-absolute-p path)
-			      (expand-file-name path)
+			      (concat "file://" (expand-file-name path))
 			      path)))
 		     ((string= type "")
 			(list nil path))
@@ -756,8 +756,7 @@ MAY-INLINE-P allows inlining it as an image."
 	 (setq thefile
 	    (let
 	       ((str (org-export-html-format-href thefile)))
-	      (if (and type (not (string= "file" type))
-		       (org-string-match-p "^//" str))
+	      (if (and type (not (string= "file" type)))
 		  (concat type ":" str)
 		  str)))
 
diff --git a/lisp/org-protocol.el b/lisp/org-protocol.el
index 3f240fd08..21f28e7ff 100644
--- a/lisp/org-protocol.el
+++ b/lisp/org-protocol.el
@@ -260,7 +260,7 @@ Here is an example:
   :group 'org-protocol
   :type '(alist))
 
-(defcustom org-protocol-default-template-key "w"
+(defcustom org-protocol-default-template-key nil
   "The default org-remember-templates key to use."
   :group 'org-protocol
   :type 'string)
diff --git a/lisp/org-src.el b/lisp/org-src.el
index 12d874e5a..d1948cc54 100644
--- a/lisp/org-src.el
+++ b/lisp/org-src.el
@@ -715,6 +715,70 @@ Org-babel commands."
      (call-interactively
       (lookup-key org-babel-map key)))))
 
+(defvar org-src-tab-acts-natively nil
+  "If non-nil, the effect of TAB in a code block is as if it were
+issued in the language major mode buffer.")
+
+(defun org-src-native-tab-command-maybe ()
+  "Perform language-specific TAB action.
+Alter code block according to effect of TAB in the language major
+mode."
+  (and org-src-tab-acts-natively
+       (org-babel-do-key-sequence-in-edit-buffer (kbd "TAB"))))
+
+(add-hook 'org-tab-first-hook 'org-src-native-tab-command-maybe)
+
+(defun org-src-font-lock-fontify-block (lang start end)
+  "Fontify code block.
+This function is called by emacs automatic fontification, as long
+as `org-src-fontify-natively' is non-nil. For manual
+fontification of code blocks see `org-src-fontify-block' and
+`org-src-fontify-buffer'"
+  (let* ((lang-mode (org-src-get-lang-mode lang))
+	 (string (buffer-substring-no-properties start end))
+	 (modified (buffer-modified-p))
+	 (org-buffer (current-buffer)) pos next)
+    (remove-text-properties start end '(face nil))
+    (with-current-buffer
+	(get-buffer-create
+	 (concat " org-src-fontification:" (symbol-name lang-mode)))
+      (delete-region (point-min) (point-max))
+      (insert string)
+      (unless (eq major-mode lang-mode) (funcall lang-mode))
+      (font-lock-fontify-buffer)
+      (setq pos (point-min))
+      (while (setq next (next-single-property-change pos 'face))
+	(put-text-property
+	 (+ start (1- pos)) (+ start next) 'face
+	 (get-text-property pos 'face) org-buffer)
+	(setq pos next)))
+    (add-text-properties
+     start end
+     '(font-lock-fontified t fontified t font-lock-multiline t))
+    (set-buffer-modified-p modified))
+  t) ;; Tell `org-fontify-meta-lines-and-blocks' that we fontified
+
+(defun org-src-fontify-block ()
+  "Fontify code block at point."
+  (interactive)
+  (save-excursion
+    (let ((org-src-fontify-natively t)
+	  (info (org-edit-src-find-region-and-lang)))
+      (font-lock-fontify-region (nth 0 info) (nth 1 info)))))
+
+(defun org-src-fontify-buffer ()
+  "Fontify all code blocks in the current buffer"
+  (interactive)
+  (org-babel-map-src-blocks nil
+    (org-src-fontify-block)))
+
+(defun org-src-get-lang-mode (lang)
+  "Return major mode that should be used for LANG.
+LANG is a string, and the returned major mode is a symbol."
+  (intern
+   (concat
+    ((lambda (l) (if (symbolp l) (symbol-name l) l))
+     (or (cdr (assoc lang org-src-lang-modes)) lang)) "-mode")))
 
 (provide 'org-src)
 
diff --git a/lisp/org-timer.el b/lisp/org-timer.el
index 33c4c0bb0..7519d8575 100644
--- a/lisp/org-timer.el
+++ b/lisp/org-timer.el
@@ -149,8 +149,7 @@ With prefix arg STOP, stop it entirely."
   "Insert a H:MM:SS string from the timer into the buffer.
 The first time this command is used, the timer is started.  When used with
 a \\[universal-argument] prefix, force restarting the timer.
-When used with a double prefix argument \
-\\[universal-argument] \\universal-argument], change all the timer string
+When used with a double prefix argument \\[universal-argument], change all the timer string
 in the region by a fixed amount.  This can be used to recalibrate a timer
 that was not started at the correct moment.
 
@@ -166,9 +165,13 @@ it in the buffer."
 (defun org-timer-value-string ()
   (format org-timer-format (org-timer-secs-to-hms (floor (org-timer-seconds)))))
 
+(defvar org-timer-timer-is-countdown nil)
 (defun org-timer-seconds ()
-  (- (org-float-time (or org-timer-pause-time (current-time)))
-     (org-float-time org-timer-start-time)))
+  (if org-timer-timer-is-countdown
+      (- (org-float-time org-timer-start-time)
+	 (org-float-time (current-time)))
+    (- (org-float-time (or org-timer-pause-time (current-time)))
+       (org-float-time org-timer-start-time))))
 
 ;;;###autoload
 (defun org-timer-change-times-in-region (beg end delta)
@@ -378,8 +381,14 @@ replace any running timer."
 		   secs nil `(lambda ()
 			       (setq org-timer-current-timer nil)
 			       (org-notify ,(format "%s: time out" hl) t)
+			       (setq org-timer-timer-is-countdown nil)
+			       (org-timer-set-mode-line 'off)
 			       (run-hooks 'org-timer-done-hook))))
-	    (run-hooks 'org-timer-set-hook))
+	    (run-hooks 'org-timer-set-hook)
+	    (setq org-timer-timer-is-countdown t
+		  org-timer-start-time
+		  (time-add (current-time) (seconds-to-time (* mins 60))))
+	    (org-timer-set-mode-line 'on))
 	(message "No timer set"))))))
 
 (provide 'org-timer)
diff --git a/lisp/org.el b/lisp/org.el
index 67ed452b0..865ccd945 100644
--- a/lisp/org.el
+++ b/lisp/org.el
@@ -5022,13 +5022,19 @@ will be prompted for."
 				'(display t invisible t intangible t))
 	t)))
 
+(defvar org-src-fontify-natively t
+  "When non-nil, fontify code in code blocks.")
+
 (defun org-fontify-meta-lines-and-blocks (limit)
   "Fontify #+ lines and blocks, in the correct ways."
   (let ((case-fold-search t))
     (if (re-search-forward
-	 "^\\([ \t]*#\\+\\(\\([a-zA-Z]+:?\\| \\|$\\)\\(_\\([a-zA-Z]+\\)\\)?\\)\\(.*\\)\\)"
+	 "^\\([ \t]*#\\+\\(\\([a-zA-Z]+:?\\| \\|$\\)\\(_\\([a-zA-Z]+\\)\\)?\\)[ \t]*\\(\\([^ \t\n]*\\)[ \t]*\\(.*\\)\\)\\)"
 	 limit t)
 	(let ((beg (match-beginning 0))
+	      (block-start (match-end 0))
+	      (block-end nil)
+	      (lang (match-string 7))
 	      (beg1 (line-beginning-position 2))
 	      (dc1 (downcase (match-string 2)))
 	      (dc3 (downcase (match-string 3)))
@@ -5053,6 +5059,7 @@ will be prompted for."
 		   (concat "^[ \t]*#\\+end" (match-string 4) "\\>.*")
 		   nil t)  ;; on purpose, we look further than LIMIT
 	      (setq end (match-end 0) end1 (1- (match-beginning 0)))
+	      (setq block-end (match-beginning 0))
 	      (when quoting
 		(remove-text-properties beg end
 					'(display t invisible t intangible t)))
@@ -5063,6 +5070,8 @@ will be prompted for."
 	      (add-text-properties end1 (+ end 1) '(face org-meta-line))
 					; for end_src
 	      (cond
+	       ((and lang org-src-fontify-natively)
+		(org-src-font-lock-fontify-block lang block-start block-end))
 	       (quoting
 		(add-text-properties beg1 (+ end1 1) '(face
 						       org-block)))
@@ -9890,6 +9899,7 @@ on the system \"/user@host:\"."
 			 (setq level (org-reduced-level
 				      (- (match-end 1) (match-beginning 1)))
 			       txt (org-link-display-format (match-string 4))
+			       txt (replace-regexp-in-string " *\[[0-9]+/[0-9]+\]$" "" txt)
 			       re (format org-complex-heading-regexp-format
 					  (regexp-quote (match-string 4))))
 			 (when org-refile-use-outline-path