If you use Obsidian, it has a nice feature where you can see a visual image of your notebook - each page is a circle, and links between are shown as lines.
Does anyone know a tool I can point at my website folders to generate such a diagram?
in particular, I’m worried there are web pages in there that nothing links to, and obvious link connections I’ve yet to make
While it doesn’t have any visual tools like that (that I know of), ahrefs’ Webmaster Tools does have a feature that can tell you if pages it finds when it crawls your website (based on a Sitemap file, for example) have no incoming links. There are a bunch of other great features in there too; might be worth checking out nonetheless.
(This is not a paid ad! 
)
I think you’d be interested in this thread where @ribose shows off a site graph tool they found.