Update directory layout and breadcrumbs

We made a few updates on the ToC that haven't been reflected on the folder structure or in breadcrumbs, e.g. Miscelanous --> Fundamentals, moving upgrade documents to what's new. Breadcrumbs are also missing things.

We can actually move the location of articles to reflect the new organization and setup redirects. We can also update breadcrumb/toc.yml based on toc.md.