Fix: openjournals/joss#1281
Builds on:

• Add missing dependencies #45
• Update default template for pandoc>=3.1.7 #46

Add support for graphviz and mermaid diagrams using https://github.com/pandoc-ext/diagram

• Vendored lua plugin bc no clean way to include it otherwise and i hate using submodules
• symlinked to filters directory
• added to default filters
• configured to enable/diable diagram engines consistent with security recs in source repo
• added deps to dockerfile
• wrote examples in example/paper.md

Works in the tex, html, and jats formats

eg. PDF:

Also added an example of how to include a highlighted code block because i thought it was weird we didn't have one

(Again sorry for non-modular PR, couldn't get the code to run otherwise)