HI Ralph,
Your second email is correct: the expectation is for first_party_sets.JSON to contain the entire list of First-Party Sets. So, each pull request would simply modify that list as needed, depending on whether some set(s) needs to be added, removed, or modified.
In practice, I think it'd be nice if our tooling ensured that the list of sets was sorted by primary domain (e.g.), but I'm not sure if we've implemented that yet. Once we've done that, you would add your new set in the corresponding position in the list, rather than at the beginning of the list.
Additionally, you're correct that the automated checks we've written are currently executed against the entire list. We'd like to enhance the tooling such that only the changes being introduced in the PR are checked, but we haven't done so yet.
Chris