I think you are confused what Github Pages is: https://pages.github.com

Specifically, my method involves using drag-and-drop .md files for the Jekyll workflow.

> Why not work directly in the version controlled cloud?

What do you do if you need to work offline? You are on a plane and forget to sync something, or for whatever reason you can't access to repository (maybe China is DDOSing GitHub again?). This is also one of my main gripes about cloud based editors, it's great if you have internet access but if you don't or you have a poor connection (e.g. public wifi) you are SOL.

I use Write (iOS) and NVAlt (OS X) which sync via Dropbox, so I always have a local copy of my notes.

> no backups to worry about

Please don't solely rely on companies to store your data. They can and do lose peoples files [0].

[0] - http://www.zdnet.com/article/dropbox-sync-glitch-results-in-...

People lose data too at a much greater frequency. if you're paranoid about Github, create crown jobs to automatically pull your repos.

Question: What benefit do you derive from using org mode format if you aren't editing it in Emacs, where you can collapse and expand?

...what do you mean... not in Emacs...

Real answer, though not who you were replying to: Org mode syntax is more appealing to me, particularly the wiki-style links. I liked it enough to use it before I used Emacs with vim-org but it was lacking so I'm happy enough editing with either Emacs on the desktop, in the browser (Github Wiki), or in Editorial (iPhone). Editorial actually does collapse/expand for Markdown so it would be nice to have that for .org files too, but I would put up with a lot of crap as long as I can work with my files in Emacs 10% of the time.

I think you are just writing markdown in .org files ^^

So the .md is technically more correct. But really the extension doesn't matter much...

No, he's writing in the syntax of Emacs org-mode, which GitHub also recognizes. Parts of it are similar to markdown, but parts are different.

For example, `markdown inline code` vs ~org-mode inline code~, and

    ```
    markdown code blocks
    ```

vs

    #+begin_src
    org-mode code blocks
    #+end_src

And [markdown links](https://daringfireball.net/projects/markdown/) vs [[http://orgmode.org/][org-mode links]].

Ah yes, I just looked quickly without reading the raw. Shoud have read the raw before writing non sense.