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This takes around 30 minutes to run on my laptop. Press ctrl-c after a few minutes to see a sub-optimal solution.
It simultaneously optimizes the paths from each port to each city, and the total number of paths used. The individual path lengths are weighted to be 1000x more important.
One remaining problem is that the objective counts each edge as one path, and minimizes the total number of used edges. However, I think we should be minimizing the total number of used nodes (which correspond to tiles). Currently it's counting a three-way junction as contributing length 3, rather than 1.