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I investigated the code a bit and found reasons of some reported issues, fixed the problems and tested on all provided polygons.
Problematic was (in most cases) duplication of a point when connecting a hole to the outer polygon. The duplicated point wasn't handled properly afterwards.
Example
A and B are a duplicated point (they have the same coordinates)
Cut line was sometimes mistakenly drawn from C to A (should be C to B) or from A to B.
Also fixed a mistakenly written line in acd2d_data.cpp in foundBoundary which caused errors.
Also added coloring of final polygons and a display option of showing point coordinates for a better visualisation and further potential debugging