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Package contents were being extracted into subdirectories of the boot tree (grub_dir, shim_dir), which meant the boot tree contained both the final boot files and the raw package extractions. Extract packages into scratch directories instead, copying only the needed files into the boot tree. This also removes the grub_dir/shim_dir instance variables and the create_dirs overrides, and moves copy_grub_modules to a standalone function in grub.py.