Fix brittle Markdown link conversion

[rg-wood]

Converting intra-project Markdown links is brittle, and can break easily. It assumes that the file name (file-name.md) will match the autogenerated anchor link. If these are not the same, the generated link will be broken. For example, if you put a # Chapter 1 heading into index.md, vellum-book will generate a broken link to the non-existent #index fragment, instead of the correct #chapter-1 one.