Add an option in the shape key menu called "Apply all shapekeys". This operator should apply all shape keys to the mesh and remove all shapekeys.
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menu mockup
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Workflow description
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Currently when you want to apply all shapekeys, you have to
1. Make "new shape from mix" (called "new shape" here)
2. Delete basis and all other shapekeys
3. finally delete "new shape"
This workflow is tricky to understand for new artists starting to work in blender.