Lesson organisation doesn't reflect URL of home page on GitHub

Re: http://carpentries.github.io/lesson-example/03-organization/index.html

The diagram here reflects what is in the `_site` folder, but the home page (created from `index.md`) as clicked from the Lesson Title header from any episode, or from the github repo page is http://carpentries.github.io/lesson-example/ rather than http://carpentries.github.io/lesson-example/index.html.

This makes the diagram more difficult to interpret, because although the two URLs are equivalent, the one that is normally seen doesn't include index.html

Start with 03-organization/index.html and compare its diagram with the home page generated from index.md and the corresponding path in _site. Confirm which URL is normally shown from the Lesson Title header and GitHub repository, then update the diagram so it reflects that URL and verify the rendered lesson page.

Written by the indexing model from the issue text.