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Re:GitHub Pages now runs Jekyll 2.2.0 by swanson on Wednesday July 30, 2014 @01:30PM (#8109706)
When you run Jekyll, it spits out an `_site` folder - which is the generated HTML/CSS/JS of your site. Locally, when you run the Jekyll server it generates the site and then serves from that folder for you to preview.

With GitHub pages, you push a repository containing the Markdown files, but not the full generated site. On GitHub's server it generates the site and then serves it. You will want to add the `_site` folder to your `.gitignore`.

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