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Libretro cores are selected based on the file extensions of the ROMs. However, ROM file extensions are not unique across cores (e.g., .zip is used in both DosBox and MAME). To load a specific core correctly, it's necessary to place the corresponding ROMs in designated folders specified in the configuration. By default, you can use the keys from cores.list as the folder names, or you can specify your own custom folder names using the 'folder' parameter for each core.