Update structure, reduce logo size

Author: supernord

assets/img/elixir-toolkit-theme_logo.svg renamed to images/elixir-toolkit-theme_logo.svg

@@ -35,7 +35,7 @@ This work is supported by the [Australian BioCommons](https://www.biocommons.org
 
 This guide makes use of the [ELIXIR toolkit theme](https://github.com/ELIXIR-Belgium/elixir-toolkit-theme)
 
-![](./assets/img/elixir-toolkit-theme_logo.svg)
+{% include image.html file="elixir-toolkit-theme_logo.svg" alt="Elixir Toolkit Theme logo" max-width="5em" %}
 
 Ideas have also been drawn from other websites using this theme including:
 - [Infectious Diseases Toolkit](https://www.infectious-diseases-toolkit.org/)

index.md

@@ -36,30 +36,57 @@ type: guides
 {:start="5"}
 5. Each new page that is included needs to be added to the `main.yml` file so that it appears in the left hand navigation menu. 
 
-An example of this code is provided below for the current How-to Guide:
+Below is the `main.yml` from the template repository:
+```yaml
+subitems:
+  - title: Home
+    url: /index
+  - title: Example page
+    url: /example_page
+  - title: Contributors
+    url: /contributors
+```
+
+To create the guide you are currently viewing, this code was updated as follows:
 
 ```yaml
 subitems:
-  - title: About
-    url: /
+  - title: Quick start
+    url: /quick_start
   - title: 1. Create a new repository
     url: /create_new
   - title: 2. Update your landing page content
     url: /update_index
   - title: 3. Add new pages to your guide
     url: /add_new_pages
-  - title: 4. Update configuration files
-    url: /structure
-  - title: 5. Test and improve your guide content
+  - title: 4. Test & improve your guide content
     url: /improve_content
-  - title: 6. Make your guide citable
+  - title: 5. Make your guide citable
     url: /zenodo
-  - title: Optional extra features
+  - title: Adding optional features
     url: /extras
+  - title: About
+    url: /
+```
+
+Note a few things:
+- The landing page url can be either `/index` or `/`
+- You can specify the order and structure of the navigation bar in `main.yml`
+- You can also add a title element and a link: this is shown below, with the `title_url` set to the landing page `index.md` for the guide
+
+```yaml
+title: Navigation bar title
+title_url: /
+subitems:
+  - title: Home
+    url: /index
+  - title: Example page
+    url: /example_page
   - title: Contributors
     url: /contributors
 ```
 
+
 There are many other options for configuring your guide web page differently and adding more complicated page and navigation structures. For more information please visit the [ELIXIR Toolkit theme documentation](https://elixir-belgium.github.io/elixir-toolkit-theme/).
 
 {% include callout.html type="important" content="You will only need to modify the `_config.yml` if you wish to make major changes to the way your new guide repository makes use of the remote ELIXIR ToolKit theme. Instructions for how to do this, and what the different options are, can be [found here](https://elixir-belgium.github.io/elixir-toolkit-theme/configuring_theme). " %}