A basic Jekyll Structure
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_includes
_layouts
assets/css
01-index.md
02-about.md
03-another.md
README.md
_config.yml

README.md

This is a basic jekyll structure. Take a look at the layout in _layouts/layout.html and the navigation snippet in _includes/_navigation.html.

Page urls are defined using the permalink frontmatter, so you can call the files whatever you like. I would recommend numbering the pages to control their order in the navigation:

01-index.md
02-about.md
03-another.md
...

I'll probably add to this as I come up with cool things to do with Jekyll.