2009-01-25 Carsten Dominik <carsten.dominik@gmail.com>

	* org-exp.el (org-export-as-html): Turn \par into a paragraph.

	* org.el (org-agenda-tags-todo-honor-ignore-options): Declare
	variable.

	* org-table.el (org-table-insert-hline): Fix typo in fuction call
	to `backward-char'.

	* org-exp.el (org-export-as-html): Remove the initial space from
	colon examples.

	* org.el (org-scan-tags): Call
	`org-agenda-check-for-timestamp-as-reason-to-ignore-todo-item'.

	* org-agenda.el (org-agenda-todo-list, org-agenda-match-view): New
	customization groups.
	(org-agenda-tags-todo-honor-ignore-options): New option.
	(org-agenda-check-for-timestamp-as-reason-to-ignore-todo-item):
	New function.
	(org-agenda-get-todos): Use
	`org-agenda-check-for-timestamp-as-reason-to-ignore-todo-item'.

2009-01-25  Carsten Dominik  <carsten.dominik@gmail.com>

	* org-exp.el (org-export-format-source-code-or-example): Escape
	HTML characters also in examples that anre not treated with
	htmlize.  Also, just switch to EXAMPLE processing if we do not
	have a good version of htmlize.

	* org-rmail.el: Fix copyright notice.

	* org.el (org-activate-footnote-links): Improve footnote link
	highlighting.

	* org-footnote.el (org-footnote-normalize): Fix finding the end of
	a footnote definition at the end of the file.

	* org-table.el (org-table-get-specials): Add an imagined hline at
	the end of the table.  This can be useful for references that want
	to go to the end of the table.  Also fix bug when computing last
	row constants, in tables that do not start right at the right
	margin.
	(org-table-eval-formula): Match and replace remove references.
	(org-table-formula-substitute-names): Make sure that names inside
	a "remote" call are left alone, the will be replaced later when
	the remote call is handled.
	(org-table-convert-refs-to-rc): Do not convert things that might
	look like a reference, but are really part of an ID or namei n a
	remote reference.
	(org-table-get-remote-range): New function.

2009-01-25  Carsten Dominik  <carsten.dominik@gmail.com>

	* org-faces.el (org-clock-overlay): Fix bug in face definition.

	* org-clock.el (org-clock-put-overlay): Use new face instead of
	`secondary-selection'.

	* org-faces.el (org-clock-overlay): New face.

2009-01-25  Carsten Dominik  <carsten.dominik@gmail.com>

	* org-exp.el (org-get-current-options): Include the option for
	publishing time stamps.

	* org.el (org-toggle-heading): Renamed from
	`org-toggel-region-headings'.
	No longer needs a region defined, but will use it if there is one.
	(org-ctrl-c-star): Simplified, relying more on the internal
	workings of `org-toggle-heading'.
	(org-toggle-item): Renamed from `org-toggle-region-items'.
	No longer needs a region defined, but will use it if there is one.
	(org-ctrl-c-minus): Simplified, relying more on the inernal
	workings of `org-toggle-item'.

	* org-export-latex.el (org-export-latex-preprocess): Fix bug in
	environment detection.  Also, do real changes only in unprotected
	places.

2009-01-25  Carsten Dominik  <carsten.dominik@gmail.com>

	* org-export-latex.el (org-export-latex-quotation-marks): Use
	`org-if-unprotected-1'.
	(org-export-latex-set-initial-vars): Check for class definition in
	property.

	* org-macs.el (org-if-unprotected-1): New macro.

2009-01-25  Carsten Dominik  <carsten.dominik@gmail.com>

	* org-compat.el (org-count-lines): New function.

	* org-exp.el (org-export-format-source-code-or-example): Handle
	switches related to text areas.

	* org.el (org-activate-footnote-links): Don't allow match inside a
	link.

	* org-footnote.el (org-footnote-re): Don't allow match inside a link.

	* org-export-latex.el (org-export-latex-links): Keep a relative
	path relative also after export.

	* org-exp.el (org-export-html-scripts): Fix HTML snippet.

	* org.el (org-make-tags-matcher): Never use IDO for completing the
	tags matcher match string.
	(org-completing-read): Also remove the special biding for "?".

	* org-attach.el (org-attach-allow-inheritance): New option.
	(org-attach-inherited): New variable.
	(org-attach-dir): Handle properties related to the attachment
	directory.
	(org-attach-check-absolute-path): New function.
	(org-attach-set-directory, org-attach-set-inherit): New commands.
	(org-attach): Accommodate the new commands in the dispatcher.

2009-01-25  Carsten Dominik  <carsten.dominik@gmail.com>

	* org-compat.el (org-fit-window-to-buffer): Fix bug with using
	`window-full-width-p'.

	* org-exp.el (org-export-as-html): Only check for images files
	that really can be inlined

	* org.el (org-image-file-name-regexp, org-file-image-p): Allow the
	list of extensions to be a parameter.

	* org-exp.el (org-export-html-inline-image-extensions): New
	variable.

	* org-agenda.el (org-prepare-agenda): Use
	`org-agenda-block-separator'.
	(org-agenda-block-separator): New option.

2009-01-25  Carsten Dominik  <carsten.dominik@gmail.com>

	* org-export-latex.el (org-export-latex-tables): Call
	`org-table-clean-before-export' with the new optional argument.

	* org-exp.el (org-table-clean-before-export): New optional
	parameter MAYBE-QUOTED, allows for quoted characters like \# in
	first column.

2009-01-25  Carsten Dominik  <carsten.dominik@gmail.com>

	* org-plot.el (org-plot/gnuplot): Fix text-ind parameter for
	histograms.

	* org-colview.el (org-colview-construct-allowed-dates): Better
	error catching when a date/time property does not have allowed
	values defined.

	* org-colview-xemacs.el (org-colview-construct-allowed-dates):
	Better error catching when a date/time property does not have
	allowed values defined.

2009-01-25  Carsten Dominik  <carsten.dominik@gmail.com>

	* org.el (org-map-entries): Restore point and restriction after
	`org-map-entries'.

2009-01-25  Carsten Dominik  <carsten.dominik@gmail.com>

	* org.el (org-time=, org-time<, org-time<=, org-time>)
	(org-time>=, org-time<>): Make sure both values are dates.

2009-01-25  Carsten Dominik  <carsten.dominik@gmail.com>

	* org-archive.el (org-extract-archive-heading): Allow %s for file
	name also in achive location heading.

2009-01-25  Carsten Dominik  <carsten.dominik@gmail.com>

	* org-archive.el (org-add-archive-files): Uniquify the list before
	returning it.

2009-01-25  Carsten Dominik  <carsten.dominik@gmail.com>

	* org-compat.el (org-fit-window-to-buffer): Use
	`window-full-width-p'.

	* org-export-latex.el (org-export-latex-fixed-width): Enforce the
	space after the colon in short examples.

	* org-exp.el (org-export-protect-colon-examples): Rewritten, to
	enforce a space after the colon.  However, we also allow lines
	that are *only* a colon.
	(org-export-as-html): Enforce the space after the colon in short
	examples.
	(org-export-preprocess-string): Do the colon example protection
	earlier.
	(org-export-remove-timestamps): Do not check for protection at the
	end of the line.

2009-01-25  Carsten Dominik  <carsten.dominik@gmail.com>

	* org.el (org-format-latex-options): Add new matcher for single
	letters between dollars.
	(org-get-header): Function removed.
	(org-heading-components): New function.

	* org-exp.el (org-export-define-heading-targets): Record ID's also
	as alternative targets.
	(org-export-as-html): Interpret "id:" links to other files by
	preserving the relative path.

	* org-jsinfo.el (org-infojs-handle-options): Catch the case if v
	is nil.

	* org-exp.el (org-export-normalize-links): Protect the main link,
	to avoid special character processing.

	* org-export-latex.el (org-export-latex-special-keyword-regexp):
	New variable.
	(org-export-latex-special-string-regexps): Variable removed.
	(org-export-latex-keywords): Use the new regexp.

	* org-exp.el (org-export-handle-include-files): Fetch switches and
	put them into the BEGIN statement.

	* org-timer.el (org-timer-mode-line-string): New variable.

	* org-clock.el (org-clock-mode-line-map): Renamed from
	`org-clock-mode-map'.
	(org-clock-mode-line-timer): Renamed from `org-mode-line-timer'.
	(org-clock-update-mode-line): Renamed from `org-update-mode-line'.
	(org-clock-put-overlay): Renamed from `org-put-clock-overlay'.
	(org-clock-remove-overlays): Renamed from
	`org-remove-clock-overlays'.

	* org-timer.el (org-timer-pause-or-continue): Implement stopping
	and mode line display.
	(org-timer-stop): New command.
	(org-timer-seconds): Return correct time when timer is paused.
	(org-timer-mode-line-timer): New variable.
	(org-timer-set-mode-line, org-timer-update-mode-line): New
	functions.

	* org.el (org-insert-heading):  Handle new value `auto' for
	`org-blank-before-new-entry'.
	(org-org-menu): Add new items for timer functions.

	* org-list.el (org-insert-item): Handle new value `auto' for
	`org-blank-before-new-entry'.

	* org.el (org-blank-before-new-entry): New value `auto', made
	default.

2009-01-25  Carsten Dominik  <carsten.dominik@gmail.com>

	* org-exp.el (org-export-normalize-links): If the link is also
	used as the description, protect the description.

2009-01-25  Carsten Dominik  <carsten.dominik@gmail.com>

	* org.el (org-closest-date): Fix bug with yearly repeats, in
	combination with preference of the past as it is used for deadline
	and scheduling search.

	* org-exp.el (org-html-handle-time-stamps): No longer check for
	the `org-export-with-timestamps' option, because the preprocesser
	has taken care of this already.

	* org.el (org-entry-properties): Catch the case when this is
	called in a non-org-mode file.

	* org-export-latex.el (org-export-latex-remove-from-headlines):
	Variable made obsolete, also LaTeX export now uses the standard
	variables.
	(org-export-as-latex): Add the timestamps parameter to the
	preprocessor parameter list.
	(org-export-latex-content): Export the remaining keywords without
	considering to remove them.
	(org-export-latex-keywords-maybe): Make the REMOVE-LIST optional.
	Use bold font instead of tt font for the keywords.
	(org-export-latex-fontify-headline): Format headlines, assuming
	that all keywords still present should be published.
	(org-export-latex-keywords): Remove argument TIMESTAMPS and just
	publish what ever remains of the time stamps.
	(org-export-latex-list-parameters): New option.
	(org-export-latex-lists): Pass additional parameters to the list
	converter.

	* org-exp.el (org-export-preprocess-string): Remove clock lines
	and timestamps already in the preprocesor.
	(org-export-remove-timestamps, org-export-remove-clock-lines): New
	functions.
	(org-export-as-ascii, org-export-as-html): Add the timestamps
	parameter to the preprocessor parameter list.

	* org-list.el (org-list-parse-list): Parse for checkboxes.
	(org-list-to-generic): Introduce and handle new parameters :cbon
	and :cboff.
	(org-list-to-latex, org-list-to-html, org-list-to-texinfo): Add
	optional parameter PARAMS.

	* org-export-latex.el (org-export-latex-special-chars): Fix
	problems with interpreting dollar signs.
	(org-inside-latex-math-p): New function.
	(org-export-latex-preprocess): Protect all the math fragments.

	* org.el (org-latex-regexps): Allow a dash after a dollar.

	* org-w3m.el (org-w3m-copy-for-org-mode): Always deactivate the
	mark after copying.

	* org-agenda.el (org-run-agenda-series): Have series options set
	when finalizing the agenda.

	* org-exp.el (org-export-format-source-code-or-example): Protect
	the converted examples.

	* org.el (org-set-regexps-and-options): Fix the regexp
	`org-complex-heading-regexp'.

2009-01-25  Carsten Dominik  <carsten.dominik@gmail.com>

	* org.el (org-edit-src-get-label-format): New function.
	(org-coderef-label-format): New option.
	(org-edit-src-code, org-edit-src-find-region-and-lang): Parse for
	a label format specification and make sure it is used in the edit
	buffer.
	(org-edit-src-get-label-format): New function.
	(org-store-link): Handle new coderef formats.
	(org-link-search): Handle new coderef formats.

	* org-footnote.el (org-footnote-create-definition)
	(org-footnote-goto-local-insertion-point): Make footnote insertion
	work correctly when the "Footnotes" headline is the last line in
	the buffer.

	* org.el (org-goto-marker-or-bmk): Expose context after jumping to
	the location.

2009-01-25  Carsten Dominik  <carsten.dominik@gmail.com>

	* org-w3m.el (org-w3m): New customization group.
	(org-w3m-deactivate-mark): New option.
	(org-w3m-copy-for-org-mode): Deactivate region, unless the user
	option say not to.

2009-01-25  Carsten Dominik  <carsten.dominik@gmail.com>

	* org.el (org-set-font-lock-defaults): Trigger footnote
	fontification.
	(org-activate-footnote-links): New function.
	(org-activate-links): New entry `footnote'.

	* org-faces.el (org-footnote): New face.

2009-01-25  Carsten Dominik  <carsten.dominik@gmail.com>

	* org-macs.el (org-re): Handle the [:word:] class.

	* org-exp.el (org-export-preprocess-string): Call
	`org-export-protect-colon-examples'.
	(org-export-protect-colon-examples): Renamed from
	`org-export-protect-examples', and scope limited to lines starting
	with a colon.

2009-01-25  Carsten Dominik  <carsten.dominik@gmail.com>

	* org-exp.el (org-export-preprocess-string): Move the preprocess
	hook to after turning on Org-mode.
	(org-export-preprocess-after-include-files-hook)
	(org-export-preprocess-after-tree-selection-hook)
	(org-export-preprocess-before-backend-specifics-hook)
	(org-export-preprocess-final-hook): New hooks.
	(org-export-preprocess-string): Run the new hooks.

	* org.el (org-ctrl-c-minus): Fix indentation for new items.

	* org-footnote.el: New file.

	* org.el (org-footnote): Require footnote code.
	(org-startup-options): Add new footnote options.
	(org-mode-map): New keybindig for footnotes.
	(org-ctrl-c-ctrl-c): Add function at footnotes.
	(org-org-menu): New menu entries for footnotes.

	* org-export-latex.el (org-export-as-latex): Pass footnote
	variable to preprocessor.
	(org-export-latex-preprocess): Treat multiple references to a
	footnote.

	* org-exp.el (org-export-preprocess-string): Call
	`org-footnote-normalize'.
	(org-export-as-ascii, org-export-as-html): Pass footnote variable
	to preprocessor.
	(org-export-as-html): Treat multiple references to a footnote.

2009-01-25  Carsten Dominik  <carsten.dominik@gmail.com>

	* org-export-latex.el (org-export-latex-links): Handle coderef
	links.

	* org.el (org-bracket-link-analytic-regexp++): New variable.
	(org-make-link-regexps): Initialize
	`org-bracket-link-analytic-regexp++'.
	(org-store-link): Implement special case in edit-src buffer.
	(org-insert-link): No use of ide to insert stored links.
	(org-link-search): Implement special case for coderefs.

	* org-exp.el (org-export-html-scripts): New constant.
	(org-export-html-style-default): Add a new style for highlighted
	code.
	(org-export-code-refs): New variable.
	(org-export-preprocess-string): Initialize `org-export-code-refs'.
	Call `org-export-replace-src-segments-and-examples'
	No longer call `org-export-protect-examples'.
	(org-export-target-internal-links): Take care of coderef targets.
	(org-export-last-code-line-counter-value): New variable.
	(org-export-replace-src-segments-and-examples): Renamed from
	`org-export-replace-src-segments', and modified.
	(org-export-format-source-code-or-example): Renamed from
	`org-export-format-source-code'.
	(org-export-number-lines): New function.
	(org-export-as-ascii, org-export-as-html): Handle coderef links.

1 files changed, 449 insertions, 132 deletions

diff --git a/lisp/org/org-exp.el b/lisp/org/org-exp.el
index 8bb77c926c8..0a888746c8c 100644
--- a/lisp/org/org-exp.el
+++ b/lisp/org/org-exp.el
@@ -5,7 +5,7 @@
 ;; Author: Carsten Dominik <carsten at orgmode dot org>
 ;; Keywords: outlines, hypermedia, calendar, wp
 ;; Homepage: http://orgmode.org
-;; Version: 6.16
+;; Version: 6.19a
 ;;
 ;; This file is part of GNU Emacs.
 ;;
@@ -34,6 +34,7 @@
 (declare-function org-agenda-skip "org-agenda" ())
 (declare-function org-infojs-options-inbuffer-template "org-jsinfo" ())
 (declare-function htmlize-region "ext:htmlize" (beg end))
+(declare-function org-id-find-id-file "org-id" (id))
 (defvar htmlize-buffer-places)  ; from htmlize.el
 
 (defgroup org-export nil
@@ -298,6 +299,24 @@ drawer names to export."
   "Hook for preprocessing an export buffer.
 Pretty much the first thing when exporting is running this hook.")
 
+(defvar org-export-preprocess-after-include-files-hook nil
+  "Hook for preprocessing an export buffer.
+This is run after the contents of included files have been inserted.")
+
+(defvar org-export-preprocess-after-tree-selection-hook nil
+  "Hook for preprocessing an export buffer.
+This is run after selection of trees to be exported has happened.
+This selection includes tags-based selection, as well as removal
+of commented and archived trees.")
+
+(defvar org-export-preprocess-before-backend-specifics-hook nil
+  "Hook run before backend-specific functions are called during preprocessing.")
+
+(defvar org-export-preprocess-final-hook nil
+  "Hook for preprocessing an export buffer.
+This is run as the last thing in the preprocessing buffer, just before
+returning the buffer string to the backend.")
+
 (defgroup org-export-translation nil
   "Options for translating special ascii sequences for the export backends."
   :tag "Org Export Translation"
@@ -381,7 +400,7 @@ This option can also be set with the +OPTIONS line, e.g. \"-:nil\"."
 (defcustom org-export-with-TeX-macros t
   "Non-nil means, interpret simple TeX-like macros when exporting.
 For example, HTML export converts \\alpha to &alpha; and \\AA to &Aring;.
-No only real TeX macros will work here, but the standard HTML entities
+Not only real TeX macros will work here, but the standard HTML entities
 for math can be used as macro names as well.  For a list of supported
 names in HTML export, see the constant `org-html-entities'.
 Not all export backends support this.
@@ -522,6 +541,31 @@ Org-mode file."
   :group 'org-export-html
   :type '(string :tag "File or URL"))
 
+(defconst org-export-html-scripts
+"<script type=\"text/javascript\">
+<!--/*--><![CDATA[/*><!--*/
+ function CodeHighlightOn(elem, id)
+ {
+   var target = document.getElementById(id);
+   if(null != target) {
+     elem.cacheClassElem = elem.className;
+     elem.cacheClassTarget = target.className;
+     target.className = \"code-highlighted\";
+     elem.className   = \"code-highlighted\";
+   }
+ }
+ function CodeHighlightOff(elem, id)
+ {
+   var target = document.getElementById(id);
+   if(elem.cacheClassElem)
+     elem.className = elem.cacheClassElem;
+   if(elem.cacheClassTarget)
+     target.className = elem.cacheClassTarget;
+ }
+/*]]>*/-->
+</script>"
+"Basic javascript that is needed by HTML files produced by Org-mode.")
+
 (defconst org-export-html-style-default
 "<style type=\"text/css\">
  <!--/*--><![CDATA[/*><!--*/
@@ -547,6 +591,8 @@ Org-mode file."
   dt { font-weight: bold; }
   div.figure { padding: 0.5em; }
   div.figure p { text-align: center; }
+  .linenr { font-size:smaller }
+  .code-highlighted {background-color:#ffff00;}
   .org-info-js_info-navigation { border-style:none; }
   #org-info-js_console-label { font-size:10px; font-weight:bold;
                                white-space:nowrap; }
@@ -647,6 +693,12 @@ be linked only."
 		 (const :tag "Always" t)
 		 (const :tag "When there is no description" maybe)))
 
+(defcustom org-export-html-inline-image-extensions
+  '("png" "jpeg" "jpg" "gif")
+  "Extensions of image files that can be inlined into HTML."
+  :group 'org-export-html
+  :type '(repeat (string :tag "Extension")))
+
 ;; FIXME: rename
 (defcustom org-export-html-expand t
   "Non-nil means, for HTML export, treat @<...> as HTML tag.
@@ -1422,6 +1474,8 @@ translations.  There is currently no way for users to extend this.")
 
 (defvar org-export-target-aliases nil
   "Alist of targets with invisible aliases.")
+(defvar org-export-code-refs nil
+  "Alist of code references and line numbers")
 
 (defun org-export-preprocess-string (string &rest parameters)
   "Cleanup STRING so that that the true exported has a more consistent source.
@@ -1442,13 +1496,12 @@ on this string to produce the exported version."
 	 target-alist rtn)
 
     (setq org-export-target-aliases nil)
+    (setq org-export-code-refs nil)
 
     (with-current-buffer (get-buffer-create " org-mode-tmp")
       (erase-buffer)
       (insert string)
       (setq case-fold-search t)
-      ;; Call the hook
-      (run-hooks 'org-export-preprocess-hook)
 
       ;; Remove license-to-kill stuff
       ;; The caller marks some stuff for killing, stuff that has been
@@ -1457,17 +1510,36 @@ on this string to produce the exported version."
 
       (let ((org-inhibit-startup t)) (org-mode))
       (setq case-fold-search t)
+
+      ;; Call the hook
+      (run-hooks 'org-export-preprocess-hook)
+
       (untabify (point-min) (point-max))
 
-      ;; Handle include files
+      ;; Handle include files, and call a hook
       (org-export-handle-include-files)
+      (run-hooks 'org-export-preprocess-after-include-files-hook)
 
-      ;; Get rid of excluded trees
+      ;; Get rid of archived trees
+      (org-export-remove-archived-trees archived-trees)
+
+      ;; Remove comment environment and comment subtrees
+      (org-export-remove-comment-blocks-and-subtrees)
+
+      ;; Get rid of excluded trees, and call a hook
       (org-export-handle-export-tags (plist-get parameters :select-tags)
 				     (plist-get parameters :exclude-tags))
+      (run-hooks 'org-export-preprocess-after-tree-selection-hook)
 
       ;; Handle source code snippets
-      (org-export-replace-src-segments)
+      (org-export-replace-src-segments-and-examples backend)
+
+      ;; Protect short examples marked by a leading colon
+      (org-export-protect-colon-examples)
+
+      ;; Normalize footnotes
+      (when (plist-get parameters :footnotes)
+	(org-footnote-normalize nil t))
 
       ;; Find all headings and compute the targets for them
       (setq target-alist (org-export-define-heading-targets target-alist))
@@ -1487,9 +1559,6 @@ on this string to produce the exported version."
 	(goto-char (point-min))
 	(insert (plist-get parameters :add-text) "\n"))
 
-      ;; Get rid of archived trees
-      (org-export-remove-archived-trees archived-trees)
-
       ;; Remove todo-keywords before exporting, if the user has requested so
       (org-export-remove-headline-metadata parameters)
 
@@ -1497,10 +1566,8 @@ on this string to produce the exported version."
       ;; but mark them as targets that should be invisible
       (setq target-alist (org-export-handle-invisible-targets target-alist))
 
-      ;; Protect examples
-      (org-export-protect-examples (if asciip 'indent nil))
-
-      ;; Protect backend specific stuff, throw away the others.
+      ;; Select and protect backend specific stuff, throw away stuff
+      ;; that is specific for other backends
       (org-export-select-backend-specific-text backend)
 
       ;; Protect quoted subtrees
@@ -1512,13 +1579,15 @@ on this string to produce the exported version."
       ;; Blockquotes and verse
       (org-export-mark-blockquote-and-verse)
 
+      ;; Remove timestamps, if the user has requested so
+      (org-export-remove-clock-lines)
+      (unless (plist-get parameters :timestamps)
+	(org-export-remove-timestamps))
+
       ;; Attach captions to the correct object
       (setq target-alist (org-export-attach-captions-and-attributes
 			  backend target-alist))
 
-      ;; Remove comment environment and comment subtrees
-      (org-export-remove-comment-blocks-and-subtrees)
-
       ;; Find matches for radio targets and turn them into internal links
       (org-export-mark-radio-links)
 
@@ -1542,22 +1611,28 @@ on this string to produce the exported version."
       (when org-export-table-remove-special-lines
 	(org-export-remove-special-table-lines))
 
-      ;; Specific LaTeX stuff
+      ;; Another hook
+      (run-hooks 'org-export-preprocess-before-backend-specifics-hook)
+
+      ;; LaTeX-specific preprocessing
       (when latexp
 	(require 'org-export-latex nil)
 	(org-export-latex-preprocess))
 
-      ;; Specific ASCII stuff
+      ;; ASCII-specific preprocessing
       (when asciip
 	(org-export-ascii-preprocess))
 
-      ;; Specific HTML stuff
+      ;; HTML-specific preprocessing
       (when htmlp
 	(org-export-html-preprocess parameters))
 
       ;; Remove or replace comments
       (org-export-handle-comments (plist-get parameters :comments))
 
+      ;; Run the final hook
+      (run-hooks 'org-export-preprocess-final-hook)
+
       (setq rtn (buffer-string)))
     (kill-buffer " org-mode-tmp")
     rtn))
@@ -1578,16 +1653,24 @@ The new targets are added to TARGET-ALIST, which is also returned."
   (org-init-section-numbers)
   (let ((re (concat "^" org-outline-regexp
 		    "\\| [ \t]*:ID:[ \t]*\\([^ \t\r\n]+\\)"))
-	level target)
+	level target last-section-target a)
     (while (re-search-forward re nil t)
       (if (match-end 1)
-	  (push (cons (org-match-string-no-properties 1)
-		      target) target-alist)
+	  (progn
+	    (push (cons (org-match-string-no-properties 1)
+			target) target-alist)
+	    (setq a (or (assoc last-section-target org-export-target-aliases)
+			(progn
+			  (push (list last-section-target)
+				org-export-target-aliases)
+			  (car org-export-target-aliases))))
+	    (push (caar target-alist) (cdr a)))
 	(setq level (org-reduced-level
 		     (save-excursion (goto-char (point-at-bol))
 				     (org-outline-level))))
 	(setq target (org-solidify-link-text
 		      (format "sec-%s" (org-section-number level))))
+	(setq last-section-target target)
 	(push (cons target target) target-alist)
 	(add-text-properties
 	 (point-at-bol) (point-at-eol)
@@ -1632,12 +1715,15 @@ the current file."
 	    (desc (match-end 2))
 	    (link (org-link-unescape (match-string 1)))
 	    (slink (org-solidify-link-text link))
-	    found props pos
+	    found props pos cref
 	    (target
 	     (cond
 	      ((cdr (assoc slink target-alist)))
 	      ((and (string-match "^id:" link)
 		    (cdr (assoc (substring link 3) target-alist))))
+	      ((string-match "^(\\(.*\\))$" link)
+	       (setq cref (match-string 1 link))
+	       (concat "coderef:" cref))
 	      ((string-match org-link-types-re link) nil)
 	      ((or (file-name-absolute-p link)
 		   (string-match "^\\." link))
@@ -1767,9 +1853,27 @@ from the buffer."
     (when (or (not todo) (not tags) (not pri))
       (goto-char (point-min))
       (while (re-search-forward re nil t)
-	(setq rpl (mapconcat (lambda (i) (if (match-end i) (match-string i) ""))
-			     elts " "))
-	(replace-match rpl t t)))))
+	(org-if-unprotected
+	 (setq rpl (mapconcat (lambda (i) (if (match-end i) (match-string i) ""))
+			      elts " "))
+	 (replace-match rpl t t))))))
+
+(defun org-export-remove-timestamps ()
+  "Remove timestamps and keywords for export."
+  (while (re-search-forward org-maybe-keyword-time-regexp nil t)
+    (backward-char 1)
+    (org-if-unprotected
+     (replace-match "")
+     (beginning-of-line 1)
+     (if (looking-at "[- \t]*\\(=>[- \t0-9:]*\\)?[ \t]*\n")
+	 (replace-match "")))))
+
+(defun org-export-remove-clock-lines ()
+  "Remove timestamps and keywords for export."
+  (let ((re (concat "^[ \t]*" org-clock-string ".*\n?")))
+    (while (re-search-forward re nil t)
+      (org-if-unprotected
+       (replace-match "")))))
 
 (defun org-export-protect-quoted-subtrees ()
   "Mark quoted subtrees with the protection property."
@@ -1789,24 +1893,25 @@ from the buffer."
 			 '(org-protected t))
     (goto-char (1+ (match-end 4)))))
 
-(defun org-export-protect-examples (&optional indent)
-  "Protect code that should be exported as monospaced examples."
-  (goto-char (point-min))
-  (while (re-search-forward "^#\\+BEGIN_EXAMPLE[ \t]*\n" nil t)
-    (goto-char (match-end 0))
-    (while (and (not (looking-at "#\\+END_EXAMPLE")) (not (eobp)))
-      (insert (if indent ":  " ":"))
-      (beginning-of-line 2)))
+(defun org-export-protect-colon-examples ()
+  "Protect lines starting with a colon."
   (goto-char (point-min))
-  (while (re-search-forward "^[ \t]*:.*\\(\n[ \t]*:.*\\)*" nil t)
-    (add-text-properties (match-beginning 0) (match-end 0)
-			 '(org-protected t))))
+  (let ((re "^[ \t]*:\\([ \t]\\|$\\)") beg end)
+    (while (re-search-forward re nil t)
+      (beginning-of-line 1)
+      (setq beg (point))
+      (while (looking-at re)
+	(end-of-line 1)
+	(or (eobp) (forward-char 1)))
+      (add-text-properties beg (if (bolp) (1- (point)) (point))
+			   '(org-protected t)))))
 
 (defun org-export-select-backend-specific-text (backend)
   (let ((formatters
 	 '((html "HTML" "BEGIN_HTML" "END_HTML")
 	   (ascii "ASCII" "BEGIN_ASCII" "END_ASCII")
 	   (latex "LaTeX" "BEGIN_LaTeX" "END_LaTeX")))
+	(case-fold-search t)
 	fmt)
 
     (while formatters
@@ -1969,10 +2074,15 @@ When it is nil, all comments will be removed."
 		    (org-translate-link
 		     (org-link-expand-abbrev (match-string 1)))))
 	      (s (concat
-		  "[[" xx "]"
+		  "[[" (org-add-props (copy-sequence xx)
+			   nil 'org-protected t)
+		  "]"
 		  (if (match-end 3)
 		      (match-string 2)
-		    (concat "[" xx "]"))
+		    (concat "[" (org-add-props
+				    (copy-sequence xx)
+				    '(org-protected t))
+			    "]"))
 		  "]")))
 	 (put-text-property 0 (length s) 'face 'org-link s)
 	 (replace-match s t t))))))
@@ -1993,8 +2103,10 @@ This is to make sure that the line-processing export backends
 can work correctly."
   (goto-char (point-min))
   (while (re-search-forward org-emph-re nil t)
-    (if (not (= (char-after (match-beginning 3))
-		(char-after (match-beginning 4))))
+    (if (and (not (= (char-after (match-beginning 3))
+		     (char-after (match-beginning 4))))
+	     (save-excursion (goto-char (match-beginning 0))
+			     (save-match-data (not (org-at-table-p)))))
 	(org-if-unprotected
 	 (subst-char-in-region (match-beginning 0) (match-end 0)
 			       ?\n ?\  t)
@@ -2149,7 +2261,7 @@ TYPE must be a string, any of:
 (defun org-export-handle-include-files ()
   "Include the contents of include files, with proper formatting."
   (let ((case-fold-search t)
-	params file markup lang start end prefix prefix1)
+	params file markup lang start end prefix prefix1 switches)
     (goto-char (point-min))
     (while (re-search-forward "^#\\+INCLUDE:?[ \t]+\\(.*\\)" nil t)
       (setq params (read (concat "(" (match-string 1) ")"))
@@ -2157,7 +2269,9 @@ TYPE must be a string, any of:
 	    prefix1 (org-get-and-remove-property 'params :prefix1)
 	    file (org-symname-or-string (pop params))
 	    markup (org-symname-or-string (pop params))
-	    lang (org-symname-or-string (pop params)))
+	    lang (and (member markup '("src" "SRC"))
+		      (org-symname-or-string (pop params)))
+	    switches (mapconcat '(lambda (x) (format "%s" x)) params " "))
       (delete-region (match-beginning 0) (match-end 0))
       (if (or (not file)
 	      (not (file-exists-p file))
@@ -2165,9 +2279,11 @@ TYPE must be a string, any of:
 	  (insert (format "CANNOT INCLUDE FILE %s" file))
 	(when markup
 	  (if (equal (downcase markup) "src")
-	      (setq start (format "#+begin_src %s\n" (or lang "fundamental"))
+	      (setq start (format "#+begin_src %s %s\n"
+				  (or lang "fundamental")
+				  (or switches ""))
 		    end "#+end_src")
-	    (setq start (format "#+begin_%s\n" markup)
+	    (setq start (format "#+begin_%s %s\n" markup switches)
 		  end  (format "#+end_%s" markup))))
 	(insert (or start ""))
 	(insert (org-get-file-contents (expand-file-name file) prefix prefix1))
@@ -2207,70 +2323,207 @@ in the list) and remove property and value from the list in LISTVAR."
       (if s (symbol-name s) s)
     s))
 
-;;; Fontification of code
-;; Currently only for the HTML backend, but who knows....
-(defun org-export-replace-src-segments ()
+;;; Fontification and line numbers for code examples
+
+(defvar org-export-last-code-line-counter-value 0)
+
+(defun org-export-replace-src-segments-and-examples (backend)
   "Replace source code segments with special code for export."
+  (setq org-export-last-code-line-counter-value 0)
   (let ((case-fold-search t)
-	lang code trans)
+	lang code trans opts)
     (goto-char (point-min))
     (while (re-search-forward
-	    "^#\\+BEGIN_SRC:?[ \t]+\\([^ \t\n]+\\)[ \t]*\n\\([^\000]+?\n\\)#\\+END_SRC.*"
+	    "\\(^#\\+BEGIN_SRC:?[ \t]+\\([^ \t\n]+\\)\\(.*\\)\n\\([^\000]+?\n\\)#\\+END_SRC.*\\)\\|\\(^#\\+BEGIN_EXAMPLE:?\\(?:[ \t]+\\(.*\\)\\)?\n\\([^\000]+?\n\\)#\\+END_EXAMPLE.*\\)"
 	    nil t)
-      (setq lang (match-string 1) code (match-string 2)
-	    trans (org-export-format-source-code lang code))
+      (if (match-end 1)
+	  ;; src segments
+	  (setq lang (match-string 2)
+		opts (match-string 3)
+		code (match-string 4))
+	(setq lang nil
+	      opts (match-string 6)
+	      code (match-string 7)))
+
+      (setq trans (org-export-format-source-code-or-example
+		   backend lang code opts))
       (replace-match trans t t))))
 
-(defvar htmlp)  ;; dynamically scoped from org-exp.el
+(defvar htmlp)  ;; dynamically scoped
+(defvar latexp)  ;; dynamically scoped
 
-(defun org-export-format-source-code (lang code)
+(defun org-export-format-source-code-or-example (backend
+						 lang code &optional opts)
   "Format CODE from language LANG and return it formatted for export.
-Currently, this only does something for HTML export, for all other
-backends, it converts the segment into an EXAMPLE segment."
+If LANG is nil, do not add any fontification.
+OPTS contains formatting optons, like `-n' for triggering numbering lines,
+and `+n' for continuing previous numering.
+Code formatting according to language currently only works for HTML.
+Numbering lines works for all three major backends (html, latex, and ascii)."
   (save-match-data
-    (cond
-     (htmlp
-      ;; We are exporting to HTML
-      (require 'htmlize nil t)
-      (if (not (fboundp 'htmlize-region-for-paste))
-	  (progn
+    (let (num cont rtn named rpllbl keepp textareap cols rows fmt)
+      (setq opts (or opts "")
+	    num (string-match "[-+]n\\>" opts)
+	    cont (string-match "\\+n\\>" opts)
+	    rpllbl (string-match "-r\\>" opts)
+	    keepp (string-match "-k\\>" opts)
+	    textareap (string-match "-t\\>" opts)
+	    cols (if (string-match "-w[ \t]+\\([0-9]+\\)" opts)
+		     (string-to-number (match-string 1 opts))
+		   80)
+	    rows (if (string-match "-h[ \t]+\\([0-9]+\\)" opts)
+		     (string-to-number (match-string 1 opts))
+		   (org-count-lines code))
+	    fmt (if (string-match "-l[ \t]+\"\\([^\"\n]+\\)\"" opts)
+		    (match-string 1 opts)))
+      (when (and textareap (eq backend 'html))
+	;; we cannot use numbering or highlighting.
+	(setq num nil cont nil lang nil))
+      (if keepp (setq rpllbl 'keep))
+      (setq rtn code)
+      (when (equal lang "org")
+	(setq rtn (with-temp-buffer
+		    (insert rtn)
+		    ;; Free up the protected lines
+		    (goto-char (point-min))
+		    (while (re-search-forward "^," nil t)
+		      (replace-match "")
+		      (end-of-line 1))
+		    (buffer-string))))
+      ;; Now backend-specific coding
+      (cond
+       ((eq backend 'html)
+	;; We are exporting to HTML
+	(when lang
+	  (require 'htmlize nil t)
+	  (when (not (fboundp 'htmlize-region-for-paste))
 	    ;; we do not have htmlize.el, or an old version of it
+	    (setq lang nil)
 	    (message
-	     "htmlize.el 1.34 or later is needed for source code formatting")
-	    (concat "#+BEGIN_EXAMPLE\n" code
-		    (if (string-match "\n\\'" code) "" "\n")
-		    "#+END_EXAMPLE\n"))
-	;; ok, we are good to go
-	(let* ((mode (and lang (intern (concat lang "-mode"))))
-	       (org-inhibit-startup t)
-	       (org-startup-folded nil)
-	       (htmltext
-		(with-temp-buffer
-		  (insert code)
-		  ;; Free up the protected stuff
-		  (goto-char (point-min))
-		  (while (re-search-forward "^," nil t)
-		    (replace-match "")
-		    (end-of-line 1))
-		  (if (functionp mode)
-		      (funcall mode)
-		    (fundamental-mode))
-		  (font-lock-fontify-buffer)
-		  (org-export-htmlize-region-for-paste
-		   (point-min) (point-max)))))
-	  (if (string-match "<pre\\([^>]*\\)>\n?" htmltext)
-	      (setq htmltext (replace-match
-			      (format "<pre class=\"src src-%s\">\n" lang)
-			      t t htmltext)))
-	  (concat "\n#+BEGIN_HTML\n" htmltext "\n#+END_HTML\n\n"))))
-     (t
-      ;; This is not HTML, so just make it an example.
-      (when (equal lang "org")
-	(while (string-match "^," code)
-	  (setq code (replace-match "" t t code))))
-      (concat "#+BEGIN_EXAMPLE\n" code
-	      (if (string-match "\n\\'" code) "" "\n")
-	      "#+END_EXAMPLE\n")))))
+	     "htmlize.el 1.34 or later is needed for source code formatting")))
+
+	(if lang
+	    (let* ((mode (and lang (intern (concat lang "-mode"))))
+		   (org-inhibit-startup t)
+		   (org-startup-folded nil))
+	      (setq rtn
+		    (with-temp-buffer
+		      (insert rtn)
+		      (if (functionp mode)
+			  (funcall mode)
+			(fundamental-mode))
+		      (font-lock-fontify-buffer)
+		      (org-export-htmlize-region-for-paste
+		       (point-min) (point-max))))
+	      (if (string-match "<pre\\([^>]*\\)>\n?" rtn)
+		  (setq rtn (replace-match
+			     (format "<pre class=\"src src-%s\">\n" lang)
+			     t t rtn))))
+	  (if textareap
+	      (setq rtn (concat
+			 (format "<p>\n<textarea cols=\"%d\" rows=\"%d\" overflow-x:scroll >\n"
+				 cols rows)
+			 rtn "</textarea>\n</p>\n"))
+	    (with-temp-buffer
+	      (insert rtn)
+	      (goto-char (point-min))
+	      (while (re-search-forward "[<>&]" nil t)
+		(replace-match (cdr (assq (char-before)
+					  '((?&."&amp;")(?<."&lt;")(?>."&gt;"))))
+			       t t))
+	      (setq rtn (buffer-string)))
+	    (setq rtn (concat "<pre class=\"example\">\n" rtn "</pre>\n"))))
+	(unless textareap
+	  (setq rtn (org-export-number-lines rtn 'html 1 1 num
+					     cont rpllbl fmt)))
+	(concat "\n#+BEGIN_HTML\n" (org-add-props rtn '(org-protected t)) "\n#+END_HTML\n\n"))
+       ((eq backend 'latex)
+	(setq rtn (org-export-number-lines rtn 'latex 0 0 num cont rpllbl fmt))
+	(concat "\n#+BEGIN_LaTeX\n"
+		(org-add-props (concat "\\begin{verbatim}\n" rtn "\n\\end{verbatim}\n")
+		    '(org-protected t))
+		"#+END_LaTeX\n\n"))
+       ((eq backend 'ascii)
+	;; This is not HTML or LaTeX, so just make it an example.
+	(setq rtn (org-export-number-lines rtn 'ascii 0 0 num cont rpllbl fmt))
+	(concat "#+BEGIN_ASCII\n"
+		(org-add-props
+		    (concat
+		     (mapconcat
+		      (lambda (l) (concat "  " l))
+		      (org-split-string rtn "\n")
+		      "\n")
+		     "\n")
+		    '(org-protected t))
+		"#+END_ASCII\n"))))))
+
+(defun org-export-number-lines (text backend
+				     &optional skip1 skip2 number cont
+				     replace-labels label-format)
+  (if (and (not number) (not (eq replace-labels 'keep)))
+      (setq replace-labels nil)) ;; must use names if no numbers
+  (setq skip1 (or skip1 0) skip2 (or skip2 0))
+  (if (not cont) (setq org-export-last-code-line-counter-value 0))
+  (with-temp-buffer
+    (insert text)
+    (goto-char (point-max))
+    (skip-chars-backward " \t\n\r")
+    (delete-region (point) (point-max))
+    (beginning-of-line (- 1 skip2))
+    (let* ((last (org-current-line))
+	   (n org-export-last-code-line-counter-value)
+	   (nmax (+ n (- last skip1)))
+	   (fmt (format "%%%dd:  " (length (number-to-string nmax))))
+	   (fm
+	    (cond
+	     ((eq backend 'html) (format "<span class=\"linenr\">%s</span>"
+					 fmt))
+	     ((eq backend 'ascii) fmt)
+	     ((eq backend 'latex) fmt)
+	     (t "")))
+	   (label-format (or label-format org-coderef-label-format))
+	   (label-pre (if (string-match "%s" label-format)
+			  (substring label-format 0 (match-beginning 0))
+			label-format))
+	   (label-post (if (string-match "%s" label-format)
+			   (substring label-format (match-end 0))
+			 ""))
+	   (lbl-re
+	    (concat 
+	     ".*?\\S-.*?\\([ \t]*\\("
+	     (regexp-quote label-pre)
+	     "\\([-a-zA-Z0-9_]+\\)"
+	     (regexp-quote label-post)
+	     "\\)\\)"))
+	   ref)
+
+      (goto-line (1+ skip1))
+      (while (and (re-search-forward "^" nil t) (not (eobp)) (< n nmax))
+	(if number
+	    (insert (format fm (incf n)))
+	  (forward-char 1))
+	(when (and (not (eq replace-labels 'keep))
+		   (looking-at lbl-re))
+	  (setq ref (match-string 3))
+	  (if replace-labels
+	      (progn
+		(delete-region (match-beginning 1) (match-end 1))
+		(push (cons ref n) org-export-code-refs))
+	    (goto-char (match-beginning 2))
+	    (delete-region (match-beginning 2) (match-end 2))
+	    (insert "(" ref ")")
+	    (push (cons ref (concat "(" ref ")")) org-export-code-refs))
+	  (when (eq backend 'html)
+	    (save-excursion
+	      (beginning-of-line 1)
+	      (insert (format "<span id=\"coderef-%s\" class=\"coderef-off\">"
+			      ref))
+	      (end-of-line 1)
+	      (insert "</span>")))))
+      (setq org-export-last-code-line-counter-value n)
+      (goto-char (point-max))
+      (newline)
+      (buffer-string))))
 
 ;;; ASCII export
 
@@ -2351,6 +2604,8 @@ underlined headlines.  The default is 3."
 		  :drawers (plist-get opt-plist :drawers)
 		  :tags (plist-get opt-plist :tags)
 		  :priority (plist-get opt-plist :priority)
+		  :footnotes (plist-get opt-plist :footnotes)
+		  :timestamps (plist-get opt-plist :timestamps)
 		  :todo-keywords (plist-get opt-plist :todo-keywords)
 		  :verbatim-multiline t
 		  :select-tags (plist-get opt-plist :select-tags)
@@ -2360,7 +2615,7 @@ underlined headlines.  The default is 3."
 		  :add-text (plist-get opt-plist :text))
 		 "\n"))
 	 thetoc have-headings first-heading-pos
-	 table-open table-buffer)
+	 table-open table-buffer link desc)
 
     (let ((inhibit-read-only t))
       (org-unmodified
@@ -2473,9 +2728,19 @@ underlined headlines.  The default is 3."
       (setq line (org-html-expand-for-ascii line))
       ;; Replace links with the description when possible
       (while (string-match org-bracket-link-regexp line)
-	(setq line (replace-match
-		    (if (match-end 3) "[\\3]" "[\\1]")
-		    t nil line)))
+	(setq link (match-string 1 line)
+	      desc (match-string (if (match-end 3) 3 1) line))
+	(if (and (> (length link) 8)
+		 (equal (substring link 0 8) "coderef:"))
+	    (setq line (replace-match
+			(format (org-export-get-coderef-format (substring link 8) desc)
+				(cdr (assoc
+				      (substring link 8)
+				      org-export-code-refs)))
+			t t line))
+	  (setq line (replace-match
+		      (if (match-end 3) "[\\3]" "[\\1]")
+		      t nil line))))
       (when custom-times
 	(setq line (org-translate-time line)))
       (cond
@@ -2719,7 +2984,8 @@ Does include HTML export options as well as TODO and CATEGORY stuff."
 #+EMAIL:     %s
 #+DATE:      %s
 #+LANGUAGE:  %s
-#+OPTIONS:   H:%d num:%s toc:%s \\n:%s @:%s ::%s |:%s ^:%s -:%s f:%s *:%s TeX:%s LaTeX:%s skip:%s d:%s todo:%s pri:%s tags:%s
+#+OPTIONS:   H:%d num:%s toc:%s \\n:%s @:%s ::%s |:%s ^:%s -:%s f:%s *:%s <:%s
+#+OPTIONS:   TeX:%s LaTeX:%s skip:%s d:%s todo:%s pri:%s tags:%s
 %s
 #+EXPORT_SELECT_TAGS: %s
 #+EXPORT_EXCLUDE_TAGS: %s
@@ -2750,6 +3016,7 @@ Does include HTML export options as well as TODO and CATEGORY stuff."
    org-export-with-special-strings
    org-export-with-footnotes
    org-export-with-emphasize
+   org-export-with-timestamps
    org-export-with-TeX-macros
    org-export-with-LaTeX-fragments
    org-export-skip-text-before-1st-heading
@@ -2933,7 +3200,8 @@ PUB-DIR is set, use this as the publishing directory."
 	 (style (concat (if (plist-get opt-plist :style-include-default)
 			    org-export-html-style-default)
 			(plist-get opt-plist :style)
-			(plist-get opt-plist :style-extra)))
+			(plist-get opt-plist :style-extra)
+			"\n" org-export-html-scripts))
 	 (html-extension (plist-get opt-plist :html-extension))
 	 (link-validate (plist-get opt-plist :link-validation-function))
 	 valid thetoc have-headings first-heading-pos
@@ -3032,6 +3300,8 @@ PUB-DIR is set, use this as the publishing directory."
 	    :todo-keywords (plist-get opt-plist :todo-keywords)
 	    :tags (plist-get opt-plist :tags)
 	    :priority (plist-get opt-plist :priority)
+	    :footnotes (plist-get opt-plist :footnotes)
+	    :timestamps (plist-get opt-plist :timestamps)
 	    :archived-trees
 	    (plist-get opt-plist :archived-trees)
 	    :select-tags (plist-get opt-plist :select-tags)
@@ -3046,7 +3316,8 @@ PUB-DIR is set, use this as the publishing directory."
 	 ind item-type starter didclose
 	 rpl path attr desc descp desc1 desc2 link
 	 snumber fnc item-tag
-	 footnotes
+	 footnotes footref-seen
+	 id-file
 	 )
 
     (let ((inhibit-read-only t))
@@ -3214,12 +3485,12 @@ lang=\"%s\" xml:lang=\"%s\">
 
 	  ;; Fixed-width, verbatim lines (examples)
 	  (when (and org-export-with-fixed-width
-		     (string-match "^[ \t]*:\\(.*\\)" line))
+		     (string-match "^[ \t]*:\\(\\([ \t]\\|$\\)\\(.*\\)\\)" line))
 	    (when (not infixed)
 	      (setq infixed t)
 	      (org-close-par-maybe)
 	      (insert "<pre class=\"example\">\n"))
-	    (insert (org-html-protect (match-string 1 line)) "\n")
+	    (insert (org-html-protect (match-string 3 line)) "\n")
 	    (when (or (not lines)
 		      (not (string-match "^[ \t]*\\(:.*\\)"
 					 (car lines))))
@@ -3236,7 +3507,6 @@ lang=\"%s\" xml:lang=\"%s\">
 		(replace-match "\\2\n"))
 	      (insert line "\n")
 	      (while (and lines
-			  (not (string-match "^[ \t]*:" (car lines)))
 			  (or (= (length (car lines)) 0)
 			      (get-text-property 0 'org-protected (car lines))))
 		(insert (pop lines) "\n"))
@@ -3308,7 +3578,7 @@ lang=\"%s\" xml:lang=\"%s\">
 
 	  ;; Format the links
 	  (setq start 0)
-	  (while (string-match org-bracket-link-analytic-regexp line start)
+	  (while (string-match org-bracket-link-analytic-regexp++ line start)
 	    (setq start (match-beginning 0))
 	    (setq path (save-match-data (org-link-unescape
 					 (match-string 3 line))))
@@ -3326,7 +3596,8 @@ lang=\"%s\" xml:lang=\"%s\">
 		  descp (and desc1 (not (equal desc1 desc2)))
 		  desc (or desc1 desc2))
 	    ;; Make an image out of the description if that is so wanted
-	    (when (and descp (org-file-image-p desc))
+	    (when (and descp (org-file-image-p
+			      desc org-export-html-inline-image-extensions))
 	      (save-match-data
 		(if (string-match "^file:" desc)
 		    (setq desc (substring desc (match-end 0)))))
@@ -3344,11 +3615,24 @@ lang=\"%s\" xml:lang=\"%s\">
 		     "\"" attr ">"
 		     (org-export-html-format-desc desc)
 		     "</a>")))
+	     ((and (equal type "id")
+		   (setq id-file (org-id-find-id-file path)))
+	      ;; This is an id: link to another file (if it was the same file,
+	      ;; it would have become an internal link...)
+	      (setq id-file (file-relative-name
+			     id-file (file-name-directory org-current-export-file)))
+	      (setq id-file (concat (file-name-sans-extension id-file)
+				    "." html-extension))
+	      (setq rpl (concat "<a href=\"" id-file "#" path "\""
+				attr ">"
+				(org-export-html-format-desc desc)
+				"</a>")))
 	     ((member type '("http" "https"))
 	      ;; standard URL, just check if we need to inline an image
 	      (if (and (or (eq t org-export-html-inline-images)
 			   (and org-export-html-inline-images (not descp)))
-		       (org-file-image-p path))
+		       (org-file-image-p
+			path org-export-html-inline-image-extensions))
 		  (setq rpl (org-export-html-format-image
 			     (concat type ":" path)))
 		(setq link (concat type ":" path))
@@ -3366,6 +3650,13 @@ lang=\"%s\" xml:lang=\"%s\">
 				(org-export-html-format-desc desc)
 				"</a>")))
 
+	     ((string= type "coderef")
+
+	      (setq rpl (format "<a href=\"#coderef-%s\" class=\"coderef\" onmouseover=\"CodeHighlightOn(this, 'coderef-%s');\" onmouseout=\"CodeHighlightOff(this, 'coderef-%s');\">%s</a>"
+				path path path
+				(format (org-export-get-coderef-format path (and descp desc))
+					(cdr (assoc path org-export-code-refs))))))
+
 	     ((functionp (setq fnc (nth 2 (assoc type org-link-protocols))))
 	      ;; The link protocol has a function for format the link
 	      (setq rpl
@@ -3385,7 +3676,9 @@ lang=\"%s\" xml:lang=\"%s\">
 			(if (functionp link-validate)
 			    (funcall link-validate filename current-dir)
 			  t))
-		  (setq file-is-image-p (org-file-image-p filename))
+		  (setq file-is-image-p
+			(org-file-image-p
+			 filename org-export-html-inline-image-extensions))
 		  (setq thefile (if abs-p (expand-file-name filename) filename))
 		  (when (and org-export-html-link-org-files-as-html
 			     (string-match "\\.org$" thefile))
@@ -3441,12 +3734,18 @@ lang=\"%s\" xml:lang=\"%s\">
 	    (while (string-match "\\([^* \t].*?\\)\\[\\([0-9]+\\)\\]" line start)
 	      (if (get-text-property (match-beginning 2) 'org-protected line)
 		  (setq start (match-end 2))
-		(let ((n (match-string 2 line)))
+		(let ((n (match-string 2 line)) extra a)
+		  (if (setq a (assoc n footref-seen))
+		      (progn
+			(setcdr a (1+ (cdr a)))
+			(setq extra (format ".%d" (cdr a))))
+		    (setq extra "")
+		    (push (cons n 1) footref-seen))
 		  (setq line
 			(replace-match
 			 (format
-			  "%s<sup><a class=\"footref\" name=\"fnr.%s\" href=\"#fn.%s\">%s</a></sup>"
-			  (match-string 1 line) n n n)
+			  "%s<sup><a class=\"footref\" name=\"fnr.%s%s\" href=\"#fn.%s\">%s</a></sup>"
+			  (match-string 1 line) n extra n n)
 			 t t line))))))
 
 	  (cond
@@ -3585,6 +3884,17 @@ lang=\"%s\" xml:lang=\"%s\">
 	     (org-export-preserve-breaks
 	      (setq line (concat line "<br/>"))))
 
+	    ;; Check if a paragraph should be started
+	    (let ((start 0))
+	      (while (and org-par-open
+			  (string-match "\\\\par\\>" line start))
+		;; Leave a space in the </p> so that the footnote matcher
+		;; does not see this.
+		(if (not (get-text-property (match-beginning 0)
+					    'org-protected line))
+		    (setq line (replace-match "</p ><p >" t t line)))
+		(setq start (match-end 0))))
+
 	    (insert line "\n")))))
 
       ;; Properly close all local lists and other lists
@@ -3693,6 +4003,15 @@ lang=\"%s\" xml:lang=\"%s\">
 	    (kill-buffer (current-buffer)))
 	(current-buffer)))))
 
+(defun org-export-get-coderef-format (path desc)
+  (save-match-data
+    (if (and desc (string-match
+		   (regexp-quote (concat "(" path ")"))
+		   desc))
+	(replace-match "%s" t t desc)
+      "%s")))
+
+
 (defun org-export-html-format-href (s)
   "Make sure the S is valid as a href reference in an XHTML document."
   (save-match-data
@@ -3881,14 +4200,18 @@ lang=\"%s\" xml:lang=\"%s\">
       (push html-table-tag html))
     (concat (mapconcat 'identity html "\n") "\n")))
 
-(defun org-table-clean-before-export (lines)
+(defun org-table-clean-before-export (lines &optional maybe-quoted)
   "Check if the table has a marking column.
 If yes remove the column and the special lines."
   (setq org-table-colgroup-info nil)
   (if (memq nil
 	    (mapcar
 	     (lambda (x) (or (string-match "^[ \t]*|-" x)
-			     (string-match "^[ \t]*| *\\([#!$*_^ /]\\) *|" x)))
+			     (string-match
+			      (if maybe-quoted
+				  "^[ \t]*| *\\\\?\\([\#!$*_^ /]\\) *|"
+				"^[ \t]*| *\\([\#!$*_^ /]\\) *|")
+			      x)))
 	     lines))
       (progn
 	(setq org-table-clean-did-remove-column nil)
@@ -4007,22 +4330,16 @@ But it has the disadvantage, that Org-mode's HTML conversions cannot be used."
   (catch 'exit
     (let (r b)
       (while (string-match org-maybe-keyword-time-regexp s)
-	(if (and (match-end 1) (equal (match-string 1 s) org-clock-string))
-	    ;; never export CLOCK
-	    (throw 'exit ""))
 	(or b (setq b (substring s 0 (match-beginning 0))))
-	(if (not org-export-with-timestamps)
-	    (setq r (concat r (substring s 0 (match-beginning 0)))
-		  s (substring s (match-end 0)))
-	  (setq r (concat
-		   r (substring s 0 (match-beginning 0))
-		   (if (match-end 1)
-		       (format "@<span class=\"timestamp-kwd\">%s @</span>"
-			       (match-string 1 s)))
-		   (format " @<span class=\"timestamp\">%s@</span>"
-			   (substring
-			    (org-translate-time (match-string 3 s)) 1 -1)))
-		s (substring s (match-end 0)))))
+	(setq r (concat
+		 r (substring s 0 (match-beginning 0))
+		 (if (match-end 1)
+		     (format "@<span class=\"timestamp-kwd\">%s @</span>"
+			     (match-string 1 s)))
+		 (format " @<span class=\"timestamp\">%s@</span>"
+			 (substring
+			  (org-translate-time (match-string 3 s)) 1 -1)))
+	      s (substring s (match-end 0))))
       ;; Line break if line started and ended with time stamp stuff
       (if (not r)
 	  s