Now it's possible to merge and subtract polygons. It works with layers and whole groups.
You will find buttons on bottom transform panel in move and select modes.
As I see it works fine with realy complex shapes even with holes.
Some details:
When you union selected layers, all selected plots, elipses and polygons will become one polygon. All layers contain old figures except one will be removed.
When you subtract, all layers except subtrahend will be modified if subtraction result is not empty, otherwise they will be deleted.