Cleaning up after merge of new variable management

# Overall title for pages.

title: "Lesson Title"

# Repository URL (without trailing slash).

repo: https://github.com/swcarpentry/lesson-example

# Root URL below username.github.io domain, with leading slash but no trailing slash.

# For example, for 'https://swcarpentry.github.io/lesson-example', use '/lesson-example'.

root: "/lesson-example"

# Contact email address.

email: lessons@software-carpentry.org

# Generic settings (should not need to change).

#------------------------------------------------------------

# Magic to make URLs resolve both locally and on GitHub.

# See https://help.github.com/articles/repository-metadata-on-github-pages/.

repository: <USERNAME>/<PROJECT>

# Sites.

amy_site: "https://amy.software-carpentry.org/workshops"

dc_site: "https://datacarpentry.org"

The master copy of each lesson would be a fork of that repo,

and each author's working copy would be a fork of that master:

![Forking Repositories]({{ site.root }}/fig/forking.svg)

![Forking Repositories]({{ site.github.url }}/fig/forking.svg)

However, GitHub only allows a user to have one fork of any particular repo.

This creates a problem for us because an author may be involved in writing several lessons,

we manually add the [template repository]({{ site.template_repo }}) as a remote called `template`

to update the lesson when the template changes.

![Repository Links]({{ site.root }}/fig/repository-links.svg)

![Repository Links]({{ site.github.url }}/fig/repository-links.svg)

## GitHub Pages

such as [R Markdown][r-markdown],

they must generate HTML or Markdown that [Jekyll][jekyll] can process

and commit that to the repository.

The [next episode]({{ site.root }}/02-formatting/) describes the Markdown we use.

The [next episode]({{ site.github.url }}/02-formatting/) describes the Markdown we use.

> ## Teaching Tools

>

To clarify what will appear where,

we store files that appear directly in the navigation bar

in the root directory of the lesson.

[The last episode]({{ site.root }}/03-organization/) describes these files.

[The last episode]({{ site.github.url }}/03-organization/) describes these files.

[github-importer]: https://import.github.com/

[jekyll]: http://jekyllrb.com/

The diagram below shows how source files and directories are laid out,

and how they are mapped to destination files and directories:

![Source and Destination Files]({{ site.root }}/fig/file-mapping.svg)

![Source and Destination Files]({{ site.github.url }}/fig/file-mapping.svg)

> ## Collections

>

> As described [earlier]({{ site.root }}/01-tooling/#collections),

> As described [earlier]({{ site.github.url }}/02-tooling/#collections),

> files that appear as top-level items in the navigation menu are stored in the root directory.

> Files that appear under the "extras" menu are stored in the `_extras` directory,

> while lesson episodes are stored in the `_episodes` directory.

The diagram below shows the internal structure of a single episode file

(click on the image to see a larger version):

<a href="{{ site.root }}/fig/episode-format.png"><img src="{{ site.root }}/fig/episode-format-small.png" alt="Formatting Rules" /></a>

<a href="{{ site.github.url }}/fig/episode-format.png"><img src="{{ site.github.url }}/fig/episode-format-small.png" alt="Formatting Rules" /></a>

## Locations and Names

where `dd` is a two-digit sequence number (with a leading 0)

and `subject` is a one- or two-word identifier.

For example,

the episodes of this example lesson are

`_episodes/01-tooling.md`

`_episodes/02-formatting.md`,

and `_episodes/03-organization.md`.

These become `/01-tooling/index.html`, `/02-formatting/index.html`, and `/03-organization/index.html` in the published site.

the first three episodes of this example lesson are

`_episodes/01-design.md`,

`_episodes/02-tooling.md`

and `_episodes/03-formatting.md`.

These become `/01-design/index.html`, `/02-tooling/index.html`, and `/03-formatting/index.html`

in the published site.

When referring to other episodes, use:

{% raw %}

    [link text]({{ site.root }}/dd-subject/)

    [link text]({{ site.github.url }}/dd-subject/)

{% endraw %}

i.e., use the episode's directory path below the site root

In order to use Jekyll and/or the checking script,

you may need to install it and some other software.

The [setup instructions]({{ site.root }}/setup/) explain what you need and how to get it.

The [setup instructions]({{ site.github.url }}/setup/) explain what you need and how to get it.

## Displaying Figures