running org-export-as-html on a subtree is currently problematic if the result
is to be merged into a document which contains html-ized versions of other
subtrees: the footnote references and definitions get clobbered.

this patch uses the CUSTOM_ID property of the subtree to generate unique
footnote references and definitions. if the subtree does not have the CUSTOM_ID
property set the result is a nop.

>From 27f89f8bfff334810aba5c33af621e351fa0be79 Mon Sep 17 00:00:00 2001
From: Suhail Shergill <suhailsherg...@gmail.com>
Date: Sun, 8 Apr 2012 10:49:51 -0400
Subject: [PATCH] org-html.el: Make footnotes unique to an entry

* lisp/org-html.el (org-export-as-html): Assign unique ids to footnotes
  if possible

If the entry (or its ancestor) has the CUSTOM_ID property defined, then
use that as part of the generated footnote references and definitions.
---
 lisp/org-html.el |   12 ++++++++----
 1 file changed, 8 insertions(+), 4 deletions(-)

diff --git a/lisp/org-html.el b/lisp/org-html.el
index c9c9d78..8b79c39 100644
--- a/lisp/org-html.el
+++ b/lisp/org-html.el
@@ -1248,6 +1248,9 @@ PUB-DIR is set, use this as the publishing directory."
 	 (org-export-have-math nil)
 	 (org-export-footnotes-seen nil)
 	 (org-export-footnotes-data (org-footnote-all-labels 'with-defs))
+	 (custom-id (or (org-entry-get nil "CUSTOM_ID" t) ""))
+	 (footnote-def-prefix (format "fn-%s" custom-id))
+	 (footnote-ref-prefix (format "fnr-%s" custom-id))
 	 (lines
 	  (org-split-string
 	   (org-export-preprocess-string
@@ -1685,8 +1688,8 @@ PUB-DIR is set, use this as the publishing directory."
 			  (format
 			   (concat "%s"
 				   (format org-export-html-footnote-format
-					   (concat "<a class=\"footref\" name=\"fnr.%s%s\" href=\"#fn.%s\">%s</a>")))
-			   (or (match-string 1 org-line) "") n extra n n)
+					   (concat "<a class=\"footref\" name=\"" footnote-ref-prefix ".%s%s\" href=\"#" footnote-def-prefix ".%s\">%s</a>")))
+			   (or (match-string 1 line) "") n extra n n)
 			  ;; If another footnote is following the
 			  ;; current one, add a separator.
 			  (if (save-match-data
@@ -1773,8 +1776,9 @@ PUB-DIR is set, use this as the publishing directory."
 			      (format
 			       (concat "<p class=\"footnote\">"
 				       (format org-export-html-footnote-format
-					       "<a class=\"footnum\" name=\"fn.%s\" href=\"#fnr.%s\">%s</a>"))
-			       n n n) t t org-line)))))
+					       (concat
+						"<a class=\"footnum\" name=\"" footnote-def-prefix ".%s\" href=\"#" footnote-ref-prefix ".%s\">%s</a>")))
+			       n n n) t t line)))))
 	    ;; Check if the line break needs to be conserved
 	    (cond
 	     ((string-match "\\\\\\\\[ \t]*$" org-line)
-- 
1.7.10

-- 
Suhail

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