Sniff out superscripts that should be footnote links

auto-footnote.js

$('sup[data-footnote]').each(function(index) {

	noteCount = $(this).html();

	$(this).html('<a id="ref' + noteCount + '" href="#note' + noteCount + '">' + noteCount + '</a>');
	
	$('#footnotes li').eq(noteCount - 1).attr('id', 'note' + noteCount).prepend('<a href="#ref' + noteCount + '">' + noteCount + '.</a> ');

});

markup.html

The footnote indicator looks like this.<sup data-footnote>1</sup>

A second one looks like this.<sup data-footnote>2</sup>

The script expects the footnotes to look like this; it could be UL or OL, up to you, just know 
the script prepends the count to the LI, so use CSS to hide the native bullets:

<ul id="footnotes">
	<li>Footnote text for the first one.</li>
	<li>Footnote text for the second one.</li>
</ul>

Before you ask, yes I have decided that un-linked footnotes in non-JS environments are fine with me.

People generally know where footnotes are going to be :)

You could also use this to generate all the link markup and then copy that back into the original content, then you'd have it without the script having to run, or I'm sure someone could make it a grunt task. I know you addressed this above, just sparked an idea :) thanks for the script.