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As far as I know, they're using Unicorn: https://github.com/blog/517-unicorn

They spin up new instances of the app and let the old instances finish serving requests before killing them.

I don't know how it works in the Rails deployment world, but for us Python/Django folks all we have to do is touch a wsgi file and/or do a soft reload of the web server for changes to be picked up, and they do so instantly. No downtime. Until then, even if files are replaced, the old site gets served (although I would recommend symlinking instead of flat-out replacing files and directories).

github uses unicorn behind nginx.