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I have found another edge case while dividing up OpenStreetMap country boundaries into QuadTiles.
I have attached the geojson in the "genericTestCase" format that @bluenote10 put together.
I am intersecting a polygon of Spain's border, which has an enclave cut out for Gibraltar, with a square tile. The Gibraltar hole is completely contained within the square tile, so should be a straight forward intersection.
This is what I expect:
This is what I get. Note the internal hole is coloured red, as it is now a part of the multipolygon