Split into cmd/cell sections. cmd json is in paragraphs, cell json is bullet points (and pending example).
Add (bullet point) section for warning flags.
Add note to `Pass::help()` about how each line should be a single `log()` call.
Also moved them to the bottom, instead of being under the "command help" heading.
Now includes more info about cells, and the custom sphinx domains/directives/roles we have.
