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AFAIK when apache gets a request like /path/to/post it looks for a file named "post" by default, not a directrory. That's why a mod rewrite rule is often added that redirects such requests to /path/to/post/ (basically just adds a trailing slash) and everything works well.
However the links in jekyll still don't have that trailing slash which confuses disqus. Comments are added to a page with the trailing slash and counters are requested for a page without the slash.
I think the pretty permalinks template should have the trailing slash to avoid the redirect and make disqus comments counters work correctly. I have it my fork http://github.com/eugenebolshakov/jekyll/tree/trailing-slashes-for-pretty-permalinks
It's obviously a tiny fix. I've also added the entire test/dest directory to .gitignore
With respect, pretty permalinks should not end with slashes. I understand why they have to in this case, and this comment isn't directed at a specific person, but the fact that Jekyll has to mangle proper URL form to appease a second-rate commenting service (Disqus is basically the Experts Exchange of comments) is a kludge, plain and simple, and it goes against everything Jekyll stands for IMO.
Jekyll's current handling of this leads to the creation of wasteful
Devs who are interested in quality Jekyll websites should shun Disqus like the plague. It's easy enough to roll your own comment support over AJAX without violating basic precepts of URL composition or wasting server resources on pointless folder-stuffing.