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various fixes in attempt to process Berlin #69

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This is still work in progress but this PR contains a range of various fixes I had to do while debugging Berlin data from @lisawink. Plenty of bugs and ton of dealing with floating point precision, which is not yet fully resolved.

The main issue we are dealing with is that poly1.difference(poly2) does not necessarily result in a correct outcome and there still might be a sliver overlap between the two. We will likely need to reconstruct the geometries in the same way I have implemented in fix_npe_edges, which was dealing with the same.

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