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One of the risks of living in a very rural place where there are no zoning rules is that your neighbor could very well do something you don't like. If you aren't comfortable with that risk, move into an uptight HOA and get on with it.
I'm making a lot of assumptions here because I don't know the painful details. But thus far this whole thing smacks of a technicality. If you remember, they applied for and were granted a modified site plan to operate the way they were. It would seem the town failed to follow some sort of open door or public notification process to the T. And this judge felt compelled to throw the book at both the town and NYST. I find the fines directed at NYST especially absurd.
Tony's right. They need to re-apply and encourage/assist the town in following procedure to the mark. Get feedback from the cranky neighbors, do your best to at least look like you are trying to mitigate those concerns.
Based on the reports I've read, the town council and administration still support the project.
That said, I'm not paying to go up there until they get this straightened out. I have no idea how the court decision would be enforced. I'm sure a Sheriff would be involved. But I have better things to do that go pay for the privilege of finding out.