[meta/PDF output] fix links and TOC

[cryptix]

This isn't about the content but the presentation. I find it really distracting that the links can't be clicked leading to a lot of scrolling or fulltext search. Additionally a table of contents and proper document outline would be very helpful since it's a lot of small sections.

@staltz what do you currently use to turn it into PDF? The tools folder only turns it into one giant markdown document AFAICT.

[cryptix]

As it stands, the only useful way to consume this document is on github itself (because of the clickable links) but here the sequence diagrams aren't rendered.

If the UML stuff is a blocker i'd wager that those should be a seperate make step and turned into images or vector graphics before being baked into the pdf.

[staltz]

I take the full markdown, open it in Obsidian, and generate a PDF. A nicer method would be to use Pandoc somehow and generate a LaTeX file, then the PDF would be beautiful.

For now, I recommend reading these docs primarily in GitHub (or locally with any IDE or Markdown editor, e.g. Obsidian or VS Code), the PDF is basically a formality to stamp the document as a tangible deliverable.