The default behavior of the magic wand, smudge, blur, sharpen, paint bucket, clone stamp tool, and healing brush tool is to sample color only from pixels on the active layer. This means you can smudge or sample in a single layer even when other layers are visible, and you can sample from one layer and paint in another one.
Alternatively, you can choose to paint using sampled data from all visible layers. For example, you can use the clone stamp tool to clone an area containing pixels from all the visible layers.
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