Improve default template structure / naming

[joepio]

The default template is a good start, but it feels at least somewhat confusing:

• The ontology website suggests to the user that that ontology is the website, but it's the ontology. Suggestion: rename to website-ontology.
• There is a website instance called Atomic Website Template, but this is not a template - it's the whole website. Suggestion: rename to website.
• There is a page instance called Atomic Website Template, but that is also not a template - it's the homepage. Suggestion: rename to homepage
• Having everything structured in a folder is OK, but it seems pretty far from ideal IMO. A folder seems too open and disorganized. IMO it would make more sense if the website instance was the actual top level parent. That is the resource that should provide structure and guidance, such as where the home page is and where the items should reside
• Not all resources are visible as subresources, which makes them effectively hidden in the sidebar.