diff --git a/lisp/ob-eval.el b/lisp/ob-eval.el
index ddad067a5..5489c0806 100644
--- a/lisp/ob-eval.el
+++ b/lisp/ob-eval.el
@@ -134,14 +134,13 @@ specifies the value of ERROR-BUFFER."
 		       current-prefix-arg
 		       shell-command-default-error-buffer
 		       t)))
-  (let ((error-file
-	 (if error-buffer
-	     (make-temp-file
-	      (expand-file-name "scor"
-                                (if (featurep 'xemacs)
-                                    (temp-directory)
-                                  temporary-file-directory)))
-	   nil))
+  (let ((input-file (org-babel-temp-file "input-"))
+	(error-file (if error-buffer (org-babel-temp-file "scor-") nil))
+	(shell-file-name
+	 (if (file-executable-p
+	      (concat (file-remote-p default-directory) shell-file-name))
+	     shell-file-name
+	   "/bin/sh"))
 	exit-status)
     (if (or replace
 	    (and output-buffer
@@ -151,12 +150,14 @@ specifies the value of ERROR-BUFFER."
 	  ;; Don't muck with mark unless REPLACE says we should.
 	  (goto-char start)
 	  (and replace (push-mark (point) 'nomsg))
+	  (write-region start end input-file)
+	  (delete-region start end)
 	  (setq exit-status
-		(call-process-region start end shell-file-name t
-				     (if error-file
-					 (list output-buffer error-file)
-				       t)
-				     nil shell-command-switch command))
+		(process-file shell-file-name input-file
+			      (if error-file
+				  (list output-buffer error-file)
+				t)
+			      nil shell-command-switch command))
 	  ;; It is rude to delete a buffer which the command is not using.
 	  ;; (let ((shell-buffer (get-buffer "*Shell Command Output*")))
 	  ;;   (and shell-buffer (not (eq shell-buffer (current-buffer)))
@@ -175,14 +176,14 @@ specifies the value of ERROR-BUFFER."
 		(progn (setq buffer-read-only nil)
 		       (delete-region (max start end) (point-max))
 		       (delete-region (point-min) (min start end))
+		       (write-region (point-min) (point-max) input-file)
+		       (delete-region (point-min) (point-max))
 		       (setq exit-status
-			     (call-process-region (point-min) (point-max)
-						  shell-file-name t
-						  (if error-file
-						      (list t error-file)
-						    t)
-						  nil shell-command-switch
-						  command)))
+			     (process-file shell-file-name input-file
+					   (if error-file
+					       (list t error-file)
+					     t)
+					   nil shell-command-switch command)))
 	      ;; Clear the output buffer, then run the command with
 	      ;; output there.
 	      (let ((directory default-directory))
@@ -192,11 +193,11 @@ specifies the value of ERROR-BUFFER."
 		      (setq default-directory directory))
 		  (erase-buffer)))
 	      (setq exit-status
-		    (call-process-region start end shell-file-name nil
-					 (if error-file
-					     (list buffer error-file)
-					   buffer)
-					 nil shell-command-switch command)))
+		    (process-file shell-file-name nil
+				  (if error-file
+				      (list buffer error-file)
+				    buffer)
+				  nil shell-command-switch command)))
 	  ;; Report the output.
 	  (with-current-buffer buffer
 	    (setq mode-line-process
@@ -230,6 +231,9 @@ specifies the value of ERROR-BUFFER."
 	    ;; (kill-buffer buffer)
 	    ))))
 
+    (when (and input-file (file-exists-p input-file))
+      (delete-file input-file))
+
     (when (and error-file (file-exists-p error-file))
       (if (< 0 (nth 7 (file-attributes error-file)))
 	  (with-current-buffer (get-buffer-create error-buffer)
diff --git a/lisp/org-agenda.el b/lisp/org-agenda.el
index 1f3ad3e5c..fce98f69e 100644
--- a/lisp/org-agenda.el
+++ b/lisp/org-agenda.el
@@ -3531,12 +3531,14 @@ generating a new one."
     (save-excursion
       (let ((inhibit-read-only t))
 	(goto-char (point-min))
-	(while (org-activate-bracket-links (point-max))
-	  (add-text-properties (match-beginning 0) (match-end 0)
-			       '(face org-link)))
-	(while (org-activate-plain-links (point-max))
-	  (add-text-properties (match-beginning 0) (match-end 0)
-			       '(face org-link)))
+	(save-excursion
+	  (while (org-activate-bracket-links (point-max))
+	    (add-text-properties (match-beginning 0) (match-end 0)
+				 '(face org-link))))
+	(save-excursion
+	  (while (org-activate-plain-links (point-max))
+	    (add-text-properties (match-beginning 0) (match-end 0)
+				 '(face org-link))))
 	(org-agenda-align-tags)
 	(unless org-agenda-with-colors
 	  (remove-text-properties (point-min) (point-max) '(face nil))))
diff --git a/lisp/org.el b/lisp/org.el
index 159b73bfb..816fb7bc1 100644
--- a/lisp/org.el
+++ b/lisp/org.el
@@ -5884,13 +5884,14 @@ needs to be inserted at a specific position in the font-lock sequence.")
 		 '(1 'org-special-keyword t)
 		 '(3 'org-property-value t))
 	   ;; Links
-	   (if (memq 'footnote lk) '(org-activate-footnote-links))
-	   (if (memq 'tag lk) '(org-activate-tags (1 'org-tag prepend)))
-	   (if (memq 'angle lk) '(org-activate-angle-links (0 'org-link t)))
-	   (if (memq 'plain lk) '(org-activate-plain-links))
-	   (if (memq 'bracket lk) '(org-activate-bracket-links (0 'org-link t)))
-	   (if (memq 'radio lk) '(org-activate-target-links (0 'org-link t)))
-	   (if (memq 'date lk) '(org-activate-dates (0 'org-date t)))
+	   (unless (or (org-in-src-block-p t) (org-in-fixed-width-region-p))
+	     (if (memq 'tag lk) '(org-activate-tags (1 'org-tag prepend)))
+	     (if (memq 'angle lk) '(org-activate-angle-links (0 'org-link t)))
+	     (if (memq 'plain lk) '(org-activate-plain-links))
+	     (if (memq 'bracket lk) '(org-activate-bracket-links (0 'org-link t)))
+	     (if (memq 'radio lk) '(org-activate-target-links (0 'org-link t)))
+	     (if (memq 'date lk) '(org-activate-dates (0 'org-date t)))
+	     (if (memq 'footnote lk) '(org-activate-footnote-links)))
 	   '("^&?%%(.*\\|<%%([^>\n]*?>" (0 'org-sexp-date t))
 	   '(org-hide-wide-columns (0 nil append))
 	   ;; TODO keyword