The Merge Visible Layers command merges the layers which are visible into a single layer. Visible layers are those which are indicated on the Layers dialog with an “eye” icon.
You can access this command from the image menubar through Image → Merge Visible Layers…,
or by using the keyboard shortcut Ctrl+M.
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You can clone onto a new empty layer. Set the clone sample source to "Current and Below" will enable you to clone from whatever is visible onto the new empty layer:
That said - using the clone tool to blend is not really the best approach for what you are doing. Masking the layers with a soft edged brush will make a better blend .
An alternative approach is described by ACP, Jesus Ramirez in his video on face replacement below: