JsClipper | Original : http : //sourceforge.net/projects/jsclipper

A bit hard to figure out what the problem is actually. Clipper (also when using SimplifyPolygons or SimplifyPolygon) can only produce weakly-simple polygons, which means that there can be pseudo-duplicate points: although sequential coordinates are quaranteed to be not indentical, some of the next points can share the same coordinate. Also a coordinate can be on the line between two points.

After simplifying (or any other boolean operation) you could make a cleaning step using Offsetting with a small negative value: https://sourceforge.net/p/jsclipper/wiki/documentation/#clipperlibclipperoffsetexecute.

This possibly removes all of the pseudo-duplicate points.

I have made also a float version of Clipper (http://jsclipper.sourceforge.net/6.4.2.2_fpoint/). It is extensively tested, but because Angus Johnson, the author of the original C# Clipper (of which JS-version is ported from), has thought that using floats causes robustness problems although according to my tests the are no such, the original C# float version does not exists. The float version is simpler to use and you can try there a small negative offset: eg. -0.001 or -0.01.

You could also give a try to PolyTree or ExPolygons (https://sourceforge.net/p/jsclipper/wiki/ExPolygons%20and%20PolyTree%206/). ExPolygons can be used to get holes and contours and PolyTree can be used to get the full parent-child-relationship of holes and contours.

The last resort is a broken-pen-nib -function. It detects all pseudo-duplicate points and make a broken-pen-nib -effect to them, so that the result is free of any duplicates. The attached images shows what this effect means using large nib-effect-value to make the effect meaning clearer. Three.js polygon triangulation fails in pseudo duplicate points. There are a discussion https://github.com/mrdoob/three.js/issues/3386 of this subject.