Docs: Use mermaid-js diagrams

[infinitymdm]

This PR has 3 goals:

1. Replace the existing static flow diagram in chapter 3 with a mermaid diagram for easier maintenance.
2. Add auto-generated documentation to each existing procedure, including a mermaid diagram explaining how the procedure works.
3. Update dependencies, READMEs, and packaging lockfiles.

This is almost purely a documentation PR, with the exception of the packaging updates in item 3.