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As it starts about 32k in, the ISO 9660 superblock doesn't inherently conflict with an Apple partition map which starts at the beginning. Apple also had proprietary ISO 9660 extensions that add extra metadata to the directory entries much like the RockRidge extension does. Those would get ignored by non-Apple implementations of ISO 9660.

Microsoft went a different route with its long filename extensions (Joliet) – they simply created a whole different (UCS-2/UTF-16 encoded) directory tree. An ISO 9660 implementation that's compatible with Joliet will prefer the Unicode directory hierarchy and look there for files.




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