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See ioctl_fat(2), FAT_IOCTL_GET_ATTRIBUTES and FAT_IOCTL_SET_ATTRIBUTES. These are numerical. The same set of attributes applies to NTFS as well, but are not exposed by ntfs-3g through this interface (ntfs-3g uses system.ntfs_attrib xattrs). This applies to Windows as well.
It has to be checked whether systems agree on the numerical values for each attribute. If systems do not agree, a common encoding has to be defined and translated as necessary. Since FAT is rare on Linux (e.g. EFI system partition, ESP), a fast short-circuit should exist (e.g. utilizing f_type of statfs, called only at boundaries).
Note: this is a separate piece of metadata compared to BSD flags and its extensions (#618).
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