This patch (for master) unifies the behaviour of GeometryTools.has2DCoordinates() and GeometryTools.has3DCoordinates().
I used tools/extractTestStats.bsh to overview all tests, removing the times and doing a \'diff\' pre/post patch shows the following:
< standard: run=644 failed=7 error=2
standard: run=688 failed=8 error=2
< smiles: run=257 failed=7 error=0
smiles: run=257 failed=7 error=1
< total: run=17733 failed=78 error=17
total: run=17777 failed=79 error=18
The extra fail on standard is due to a test which will randomly fail (will post bug on this) and the other error on smiles was from a timeout.