Babel now cleans up any temporary files created using org-babel-temp-file

* lisp/ob.el (org-babel-temporary-directory): variable to hold the
  value of the Babel temporary directory

  (org-babel-temp-file): replacement for make-temp-file with cleanup
  on exit of Emacs

  (org-babel-remove-temporary-directory): cleanup function run on exit
  of Emacs

  (kill-emacs-hook): now includes babel cleanup function

* lisp/ob-C.el (org-babel-C-execute): using org-babel-temp-file
  instead of make-temp-file

* lisp/ob-R.el (org-babel-R-assign-elisp): using `org-babel-temp-file'
  instead of `make-temp-file'

  (org-babel-R-evaluate-external-process): using `org-babel-temp-file'
  instead of `make-temp-file'

  (org-babel-R-evaluate-session): using `org-babel-temp-file' instead of
  `make-temp-file'

* lisp/ob-asymptote.el (org-babel-execute:asymptote): using
  `org-babel-temp-file' instead of `make-temp-file'

* lisp/ob-clojure.el (org-babel-clojure-evaluate-external-process):
  using `org-babel-temp-file' instead of `make-temp-file'

* lisp/ob-ditaa.el (org-babel-execute:ditaa): using
  `org-babel-temp-file' instead of `make-temp-file'

* lisp/ob-dot.el (org-babel-execute:dot): using `org-babel-temp-file'
  instead of `make-temp-file'

* lisp/ob-gnuplot.el (org-babel-gnuplot-process-vars): using
  `org-babel-temp-file' instead of `make-temp-file'

  (org-babel-execute:gnuplot): using `org-babel-temp-file' instead of
  `make-temp-file'

* lisp/ob-haskell.el (org-babel-load-session:haskell): using
  `org-babel-temp-file' instead of `make-temp-file'

  (org-babel-haskell-export-to-lhs): using `org-babel-temp-file' instead
  of `make-temp-file'

* lisp/ob-latex.el (org-babel-execute:latex): using
  `org-babel-temp-file' instead of `make-temp-file'

* lisp/ob-ledger.el (org-babel-execute:ledger): using
  `org-babel-temp-file' instead of `make-temp-file'

* lisp/ob-lisp.el (org-babel-execute:lisp): using
  `org-babel-temp-file' instead of `make-temp-file'

* lisp/ob-octave.el (org-babel-octave-evaluate-external-process):
  using `org-babel-temp-file' instead of `make-temp-file'

  (org-babel-octave-evaluate-session): using `org-babel-temp-file'
  instead of `make-temp-file'

  (org-babel-octave-import-elisp-from-file): using `org-babel-temp-file'
  instead of `make-temp-file'

* lisp/ob-perl.el (org-babel-perl-evaluate): using
  `org-babel-temp-file' instead of `make-temp-file'

* lisp/ob-python.el (org-babel-python-evaluate): using
  `org-babel-temp-file' instead of `make-temp-file'
  using `org-babel-temp-file' instead of `make-temp-file'

* lisp/ob-ruby.el (org-babel-ruby-evaluate): using
  `org-babel-temp-file' instead of `make-temp-file'
  using `org-babel-temp-file' instead of `make-temp-file'

* lisp/ob-sass.el (org-babel-execute:sass): using
  `org-babel-temp-file' instead of `make-temp-file'

* lisp/ob-sh.el (org-babel-sh-evaluate): using `org-babel-temp-file'
  instead of `make-temp-file'

* lisp/ob-sql.el (org-babel-execute:sql): using `org-babel-temp-file'
  instead of `make-temp-file'

* lisp/ob-sqlite.el (org-babel-execute:sqlite): using
  `org-babel-temp-file' instead of `make-temp-file'

  (org-babel-sqlite-expand-vars): using `org-babel-temp-file' instead of
   `make-temp-file'

lisp/ob-C.el

@@ -84,12 +84,12 @@ header arguments (calls `org-babel-C-expand')."
   "This function should only be called by `org-babel-execute:C'
 or `org-babel-execute:c++'."
   (let* ((processed-params (org-babel-process-params params))
-         (tmp-src-file (make-temp-file "org-babel-C-src" nil
+         (tmp-src-file (org-babel-temp-file "C-src-" nil
                                        (cond
 					((equal org-babel-c-variant 'c) ".c")
 					((equal org-babel-c-variant 'cpp) ".cpp"))))
-         (tmp-bin-file (make-temp-file "org-babel-C-bin"))
-         (tmp-out-file (make-temp-file "org-babel-C-out"))
+         (tmp-bin-file (org-babel-temp-file "C-bin-"))
+         (tmp-out-file (org-babel-temp-file "C-out-"))
          (cmdline (cdr (assoc :cmdline params)))
          (flags (cdr (assoc :flags params)))
          (full-body (org-babel-C-expand body params))
@@ -108,7 +108,7 @@ or `org-babel-execute:c++'."
     ((lambda (results)
        (org-babel-reassemble-table
 	(if (member "vector" (nth 2 processed-params))
-	    (let ((tmp-file (make-temp-file "ob-c")))
+	    (let ((tmp-file (org-babel-temp-file "c-")))
 	      (with-temp-file tmp-file (insert results))
 	      (org-babel-import-elisp-from-file tmp-file))
 	  (org-babel-read results))

lisp/ob-R.el

@@ -139,7 +139,7 @@ This function is called by `org-babel-execute-src-block'."
 (defun org-babel-R-assign-elisp (name value colnames-p rownames-p)
   "Construct R code assigning the elisp VALUE to a variable named NAME."
   (if (listp value)
-      (let ((transition-file (make-temp-file "org-babel-R-import")))
+      (let ((transition-file (org-babel-temp-file "R-import-")))
         ;; ensure VALUE has an orgtbl structure (depth of at least 2)
         (unless (listp (car value)) (setq value (list value)))
         (with-temp-file (org-babel-maybe-remote-file transition-file)
@@ -235,7 +235,7 @@ string. If RESULT-TYPE equals 'value then return the value of the
 last statement in BODY, as elisp."
   (case result-type
     (value
-     (let ((tmp-file (make-temp-file "org-babel-R-results-")))
+     (let ((tmp-file (org-babel-temp-file "R-results-")))
        (org-babel-eval org-babel-R-command
 		       (format org-babel-R-wrapper-method
 			       body tmp-file
@@ -256,7 +256,7 @@ string. If RESULT-TYPE equals 'value then return the value of the
 last statement in BODY, as elisp."
   (case result-type
     (value
-     (let ((tmp-file (make-temp-file "org-babel-R"))
+     (let ((tmp-file (org-babel-temp-file "R-"))
 	   broke)
        (org-babel-comint-with-output (session org-babel-R-eoe-output)
 	 (insert (mapconcat

lisp/ob-asymptote.el

@@ -73,7 +73,7 @@ This function is called by `org-babel-execute-src-block'."
                           (match-string 1 out-file))
                      "pdf"))
          (cmdline (cdr (assoc :cmdline params)))
-         (in-file (make-temp-file "org-babel-asymptote"))
+         (in-file (org-babel-temp-file "asymptote-"))
          (cmd (concat "asy "
                       (if out-file
                           (concat "-globalwrite -f " format " -o " out-file)

lisp/ob-clojure.el

@@ -261,7 +261,7 @@ repl buffer."
 				       " "))))
     (case result-type
       (output (org-babel-eval cmd body))
-      (value (let* ((tmp-file (make-temp-file "org-babel-clojure-results-")))
+      (value (let* ((tmp-file (org-babel-temp-file "clojure-results-")))
 	       (org-babel-eval cmd (format org-babel-clojure-wrapper-method
 					   body tmp-file tmp-file))
 	       (org-babel-clojure-table-or-string

lisp/ob-ditaa.el

@@ -53,7 +53,7 @@ This function is called by `org-babel-execute-src-block'."
   (let ((result-params (split-string (or (cdr (assoc :results params)) "")))
         (out-file (cdr (assoc :file params)))
         (cmdline (cdr (assoc :cmdline params)))
-        (in-file (make-temp-file "org-babel-ditaa")))
+        (in-file (org-babel-temp-file "ditaa-")))
     (unless (file-exists-p org-ditaa-jar-path)
       (error "Could not find ditaa.jar at %s" org-ditaa-jar-path))
     (with-temp-file in-file (insert body))

lisp/ob-dot.el

@@ -70,7 +70,7 @@ This function is called by `org-babel-execute-src-block'."
         (out-file (cdr (assoc :file params)))
         (cmdline (cdr (assoc :cmdline params)))
         (cmd (or (cdr (assoc :cmd params)) "dot"))
-        (in-file (make-temp-file "org-babel-dot")))
+        (in-file (org-babel-temp-file "dot-")))
     (with-temp-file in-file
       (insert (org-babel-expand-body:dot body params processed-params)))
     (org-babel-eval (concat cmd " " in-file " " cmdline " -o " out-file) "")

lisp/ob-gnuplot.el

@@ -68,7 +68,7 @@ code."
       (car pair) ;; variable name
       (if (listp (cdr pair)) ;; variable value
           (org-babel-gnuplot-table-to-data
-           (cdr pair) (make-temp-file "org-babel-gnuplot") params)
+           (cdr pair) (org-babel-temp-file "gnuplot") params)
         (cdr pair))))
    (org-babel-ref-variables params)))
 
@@ -141,7 +141,7 @@ This function is called by `org-babel-execute-src-block'."
     (save-window-excursion
       ;; evaluate the code body with gnuplot
       (if (string= session "none")
-          (let ((script-file (make-temp-file "org-babel-gnuplot-script")))
+          (let ((script-file (org-babel-temp-file "gnuplot-script")))
             (with-temp-file script-file
               (insert (concat body "\n")))
             (message "gnuplot \"%s\"" script-file)

lisp/ob-haskell.el

@@ -116,7 +116,7 @@ then create one.  Return the initialized session."
   (save-window-excursion
     (let* ((buffer (org-babel-prep-session:haskell
 		    session params processed-params))
-           (load-file (concat (make-temp-file "org-babel-haskell-load") ".hs")))
+           (load-file (concat (org-babel-temp-file "haskell-load-") ".hs")))
       (with-temp-buffer
         (insert body) (write-file load-file)
         (haskell-mode) (inferior-haskell-load-file))
@@ -177,7 +177,7 @@ constructs (header arguments, no-web syntax etc...) are ignored."
           (concat "^\\([ \t]*\\)#\\+begin_src[ \t]haskell*\\(.*\\)?[\r\n]"
                   "\\([^\000]*?\\)[\r\n][ \t]*#\\+end_src.*"))
          (base-name (file-name-sans-extension (buffer-file-name)))
-         (tmp-file (make-temp-file "ob-haskell"))
+         (tmp-file (org-babel-temp-file "haskell-"))
          (tmp-org-file (concat tmp-file ".org"))
          (tmp-tex-file (concat tmp-file ".tex"))
          (lhs-file (concat base-name ".lhs"))

lisp/ob-latex.el

@@ -70,7 +70,7 @@ This function is called by `org-babel-execute-src-block'."
   (setq body (org-babel-expand-body:latex body params))
   (if (cdr (assoc :file params))
       (let* ((out-file (cdr (assoc :file params)))
-	     (tex-file (make-temp-file "org-babel-latex" nil ".tex"))
+	     (tex-file (org-babel-temp-file "latex-" nil ".tex"))
 	     (border (cdr (assoc :border params)))
 	     (fit (or (cdr (assoc :fit params)) border))
 	     (height (and fit (cdr (assoc :pdfheight params))))

lisp/ob-ledger.el

@@ -50,8 +50,8 @@ called by `org-babel-execute-src-block'."
   (message "executing Ledger source code block")
   (let ((result-params (split-string (or (cdr (assoc :results params)) "")))
 	(cmdline (cdr (assoc :cmdline params)))
-        (in-file (make-temp-file "org-babel-ledger"))
-	(out-file (make-temp-file "org-babel-ledger-output"))
+        (in-file (org-babel-temp-file "ledger-"))
+	(out-file (org-babel-temp-file "ledger-output-"))
 	)
     (with-temp-file in-file (insert body))
     (message (concat "ledger -f " in-file " " cmdline))

lisp/ob-lisp.el

@@ -74,7 +74,7 @@ This function is called by `org-babel-execute-src-block'"
          (save-window-excursion
            (cadr (slime-eval `(swank:eval-and-grab-output ,full-body))))
        ;; external evaluation
-       (let ((script-file (make-temp-file "ob-lisp-script")))
+       (let ((script-file (org-babel-temp-file "lisp-script-")))
          (with-temp-file script-file
            (insert
             ;; return the value or the output

lisp/ob-octave.el

@@ -178,7 +178,7 @@ value of the last statement in BODY, as elisp."
 	       org-babel-octave-shell-command)))
     (case result-type
       (output (org-babel-eval cmd body))
-      (value (let ((tmp-file (make-temp-file "org-babel-results-")))
+      (value (let ((tmp-file (org-babel-temp-file "results-")))
 	       (org-babel-eval
 		cmd
 		(format org-babel-octave-wrapper-method body tmp-file tmp-file))
@@ -188,8 +188,8 @@ value of the last statement in BODY, as elisp."
 (defun org-babel-octave-evaluate-session
   (session body result-type &optional matlabp)
   "Evaluate BODY in SESSION."
-  (let* ((tmp-file (make-temp-file "org-babel-results-"))
-	 (wait-file (make-temp-file "org-babel-matlab-emacs-link-wait-signal-"))
+  (let* ((tmp-file (org-babel-temp-file "results-"))
+	 (wait-file (org-babel-temp-file "matlab-emacs-link-wait-signal-"))
 	 (full-body
 	  (case result-type
 	    (output
@@ -246,7 +246,7 @@ value of the last statement in BODY, as elisp."
   "Import data from FILE-NAME.
 This removes initial blank and comment lines and then calls
 `org-babel-import-elisp-from-file'."
-  (let ((temp-file (make-temp-file "org-babel-results-")) beg end)
+  (let ((temp-file (org-babel-temp-file "results-")) beg end)
     (with-temp-file temp-file
       (insert-file-contents file-name)
       (re-search-forward "^[ \t]*[^# \t]" nil t)

lisp/ob-perl.el

@@ -107,7 +107,7 @@ return the value of the last statement in BODY, as elisp."
   (when session (error "Sessions are not supported for Perl."))
   (case result-type
     (output (org-babel-eval org-babel-perl-command body))
-    (value (let ((tmp-file (make-temp-file "org-babel-perl-results-")))
+    (value (let ((tmp-file (org-babel-temp-file "perl-results-")))
 	     (org-babel-eval
 	      org-babel-perl-command
 	      (format org-babel-perl-wrapper-method body tmp-file))

lisp/ob-python.el

@@ -203,7 +203,7 @@ return the value of the last statement in BODY, as elisp."
       ;; external process evaluation
       (case result-type
 	(output (org-babel-eval org-babel-python-command body))
-	(value (let ((tmp-file (make-temp-file "org-babel-python-results-")))
+	(value (let ((tmp-file (org-babel-temp-file "python-results-")))
 		 (org-babel-eval org-babel-python-command
 				 (format
 				  (if (member "pp" result-params)
@@ -251,7 +251,7 @@ return the value of the last statement in BODY, as elisp."
 	    (if (or (member "code" result-params) (member "pp" result-params))
 		results
 	      (org-babel-python-table-or-string results)))
-	  (let ((tmp-file (make-temp-file "org-babel-python-results-")))
+	  (let ((tmp-file (org-babel-temp-file "python-results-")))
 	    (org-babel-comint-with-output
 		(buffer org-babel-python-eoe-indicator t body)
 	      (let ((comint-process-echoes nil))

lisp/ob-ruby.el

@@ -186,7 +186,7 @@ return the value of the last statement in BODY, as elisp."
       ;; external process evaluation
       (case result-type
 	(output (org-babel-eval org-babel-ruby-command body))
-	(value (let ((tmp-file (make-temp-file "org-babel-ruby-results-")))
+	(value (let ((tmp-file (org-babel-temp-file "ruby-results-")))
 		 (org-babel-eval org-babel-ruby-command
 				 (format (if (member "pp" result-params)
 					     org-babel-ruby-pp-wrapper-method
@@ -221,7 +221,7 @@ return the value of the last statement in BODY, as elisp."
 	  (if (or (member "code" result-params) (member "pp" result-params))
 	      results
 	    (org-babel-ruby-table-or-string results)))
-	(let* ((tmp-file (make-temp-file "org-babel-ruby-results-"))
+	(let* ((tmp-file (org-babel-temp-file "ruby-results-"))
 	       (ppp (or (member "code" result-params)
 			(member "pp" result-params))))
 	  (org-babel-comint-with-output

lisp/ob-sass.el

@@ -51,9 +51,9 @@
 This function is called by `org-babel-execute-src-block'."
   (let* ((result-params (split-string (or (cdr (assoc :results params)) "")))
          (file (cdr (assoc :file params)))
-         (out-file (or file (make-temp-file "org-babel-sass-out")))
+         (out-file (or file (org-babel-temp-file "sass-out-")))
          (cmdline (cdr (assoc :cmdline params)))
-         (in-file (make-temp-file "org-babel-sass-in"))
+         (in-file (org-babel-temp-file "sass-in-"))
          (cmd (concat "sass " (or cmdline "") in-file " " out-file)))
     (with-temp-file in-file
       (insert (org-babel-expand-body:sass body params))) (shell-command cmd)

lisp/ob-sh.el

@@ -155,12 +155,12 @@ return the value of the last statement in BODY."
      (if (or (member "scalar" result-params)
 	     (member "output" result-params))
 	 results
-       (let ((tmp-file (make-temp-file "org-babel-sh")))
+       (let ((tmp-file (org-babel-temp-file "sh-")))
 	 (with-temp-file tmp-file (insert results))
 	 (org-babel-import-elisp-from-file tmp-file))))
    (if (not session)
        (org-babel-eval org-babel-sh-command (org-babel-trim body))
-     (let ((tmp-file (make-temp-file "org-babel-sh")))
+     (let ((tmp-file (org-babel-temp-file "sh-")))
        (mapconcat
 	#'org-babel-sh-strip-weird-long-prompt
 	(mapcar

lisp/ob-sql.el

@@ -60,9 +60,9 @@ This function is called by `org-babel-execute-src-block'."
 	 (processed-params (org-babel-process-params params))
          (cmdline (cdr (assoc :cmdline params)))
          (engine (cdr (assoc :engine params)))
-         (in-file (make-temp-file "org-babel-sql-in"))
+         (in-file (org-babel-temp-file "sql-in-"))
          (out-file (or (cdr (assoc :out-file params))
-                       (make-temp-file "org-babel-sql-out")))
+                       (org-babel-temp-file "sql-out-")))
          (command (case (intern engine)
                     ('mysql (format "mysql %s -e \"source %s\" > %s"
                                     (or cmdline "") in-file out-file))

lisp/ob-sqlite.el

@@ -73,7 +73,7 @@ This function is called by `org-babel-execute-src-block'."
 			    (insert (org-babel-expand-body:sqlite
 				     body nil (list nil vars))))
 			  sql-file)
-			(make-temp-file "ob-sqlite-sql")))
+			(org-babel-temp-file "sqlite-sql-")))
 	  (cons "cmd" org-babel-sqlite3-command)
 	  (cons "header" (if headers-p "-header" "-noheader"))
 	  (cons "separator"
@@ -117,7 +117,7 @@ This function is called by `org-babel-execute-src-block'."
 							el
 						      (format "%S" el)))))))
 		      data-file)
-		    (make-temp-file "ob-sqlite-data"))
+		    (org-babel-temp-file "sqlite-data-"))
 		 (if (stringp val) val (format "%S" val))))
 	     (cdr pair))
 	    body)))

lisp/ob.el

@@ -1658,6 +1658,31 @@ the remote connection."
         (concat "/" user (when user "@") host ":" file))
     file))
 
+(defvar org-babel-temporary-directory
+  (or (and (boundp 'org-babel-temporary-directory)
+	   org-babel-temporary-directory)
+      (make-temp-file "babel-" t))
+  "Directory to hold temporary files created to execute code blocks.
+Used by `org-babel-temp-file'.  This directory will be removed on
+Emacs shutdown.")
+
+(defun org-babel-temp-file (prefix &optional suffix)
+  "Create a temporary file in the `org-babel-temporary-directory'.
+Passes PREFIX and SUFFIX directly to `make-temp-file' with the
+value of `temporary-file-directory' temporarily set to the value
+of `org-babel-temporary-directory'."
+  (let ((temporary-file-directory (expand-file-name
+				   org-babel-temporary-directory
+				   temporary-file-directory)))
+    (make-temp-file prefix suffix)))
+
+(defun org-babel-remove-temporary-directory ()
+  "Remove `org-babel-temporary-directory' on Emacs shutdown."
+  (when (boundp 'org-babel-temporary-directory)
+    (delete-directory org-babel-temporary-directory t)))
+
+(add-hook 'kill-emacs-hook 'org-babel-remove-temporary-directory)
+
 (provide 'ob)
 
 ;; arch-tag: 01a7ebee-06c5-4ee4-a709-e660d28c0af1