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The Clipper library has difficulties processing overlapping polygons. Namely, the function Clipper::JoinCommonEdges() has potentially a terrible time complexity if the output of the operation is of the PolyTree type. This function implmenets a following workaround: 1) Peform the Clipper operation with the output to Paths. This method handles overlaps in a reasonable time. 2) Run Clipper Union once again to extract the PolyTree from the result of 1).