Markdown links now behave inline with other renderers

As requested, this PR is a cleaned up version of just the linking changes.

Additionally, I made it so that you *must* include .md. This is because other renderers like GitHub or even in IDE editors are looking for a .md file, not the extension-less URL. This PR keeps the nice URLs on the generated web pages, but leaves the markdown files themselves fully functional.

See: https://github.com/veonik/codex/blob/md-links/public/docs/codex/1.0/getting-started/navigation.md
and: https://github.com/veonik/codex/blob/md-links/public/docs/codex/1.0/toc.md