It’s not much, but I finally found some semblance of a reason or rationale for Jekyll’s wasteful
/foo/index.html folder structures in the form of this pull request from 2009.
AFAIK when apache gets a request like /path/to/post it looks for a file named “post” by default, not a directory. 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