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Is it not possible to layer_get_id on the layer folders? I'd like to have set the visible flag on a whole group at once... though I can just use a different kind of layer as the 'base' layer if that's the case.
It's strange that you can toggle visibility on them in the IDE - is this purely convenience, and really just hiding its child layers individually? I noticed the same, if I make an instance layer, then 2 sublayers, layer_set_visible on the parent 'instance' layer doesn't hide the children.