[checkoutlinesufo] improve overlap removal #1146
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- removing overlap can leave coincident (or very near coincident) points. When those points are at the contour start point (as determined by `restore_contour_order`), this can cause a crash when `contour.setStartPoint` is called more than once. - updated test data that was affected (in a very minor way) by the above change - added warning for dropping support of "hybrid" UFO2-as-UFO3
- update `ufotools.thresholdAttrGlyph` method to preserve 'smooth' attribute in points after ThresholdPen which can revert some cases. Preservation is done by contour index + coordinate rather than point index, since ThresholdPen can remove points (invalidating index-based tracking) - revert test data to original form
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closes #790