This premise is wrong. The break up will be state by state and the war will be regional. The city vs state thing is bogus. Cities have to go with the state. If a state secedes from the union then all the cities in that state secedes.
Who said anything about secession? Last time, secession was the trigger for the war, because the issues being debated were tied to geography, but it is not necessary for a civil war to erupt. This time, the issues have nothing to do with a dispute over state laws or policies; it’s strictly ideological, and to the extent there is any geographical divide, it is as the article states: urban vs rural. It will be the “Clinton Archipelago” against “Trumpland”.
According to whose rules?! The problem with trying to out-guess a nightmare is that the nightmare is undefined. You can't predict chaos.
For instance, in my state (Washington) Seattle is a lefty loony-bin literally surrounded on all sides by the right. In the event of a civil war smaller internecine warfare would develop between the two factions, drawn down ideological lines (as well as geographical ones).
Already surrounded, Seattle would be likely be quarantined. But that's all conjecture because we don't (can't) know how the dominoes will fall.
i disagree ... i believe state boundaries/governments will be as totally meaningless as they have already become
Totally disagree. This will be far more like part of the First American Revolution, which was actually two wars. The war of the States against Britain, and war of the Patriots vs. the Royalists. The next American War will be like the latter. And the big split WILL be rural vs. urban.