Directory structure is not triggered by flags in linkml

[cmiddi]

A tactical amendment has been made to allow for the generation of the site documentation for Classes, Slots, Enums and Types to be made into sub-directories to allow govuk-mkdocs navigation menu to be built into categories. The markdown generator within linkml needs to be amended so this isn't mandatory and could be triggered as a command line option.

[galund]

We think we may undo this change, as we're now planning to construct the menu by hand.

Considerations:

• there are a number of manually-created internal links (usually in the description field but potentially elsewhere eg in see_also) and these will need to be fixed
• we should consider whether there should be an index file as a replacement for the navigation menu, so that there is still an ordered list of all the things somewhere

Any other thoughts on requirements here @cmiddi ?