The Clone brush in AE should automatically reveal only the clone brush strokes in the comp window when Paint on Transparent is active but still have the layer source visible in teh layer window. Currently it completely disappears in the both windows and you need to manually select another duplicated layer as the clone source for EVERY single clone brush stroke. While you can set the source in the Paint panel, you can't paint with the Paint on transparent active as the Layer window is fully black. The current method is cumbersome and completely counter-intuitive.
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