File System
Atari TOS uses GEMDOS which uses a modified FAT12 (or, on hard disks, FAT16) file system. The major differences are the fact that the boot sector does not need to contain the IBM compatible jump sequence at the beginning (typically 0xe9 xx xx or 0xeb xx 90), the lack (before TOS 1.04) of an OEM Identifier compatible with PC-based systems, and the fact that a checksum is used to mark the boot sector as executable (the PC format uses the signature word 0x55 aa instead). Executable boot sectors for the Atari platform typically start with an MC68K jump opcode (e.g. 0x603c), and the last two byte word must sum with the rest of the boot sector (in big-endian word form) to 0x1234 in order to be bootable.
Unlike MS-DOS, GEMDOS would typically allow disks with unusual sector and track counts, so disks with 10 or even 11 sectors per track and over 80 formatted tracks were not uncommon in the Atari community. Typically a safe combination, 10 sectors per track by 80 tracks, was used, yielding an unformatted capacity of 800KB, but many users pushed the capacity of their double density disks up over 900KB using custom formats.
GEMDOS disc file systems can be read using MS-DOS or MS-Windows 95. Later systems from Microsoft have incompatibilities.
CP/M was considered originally but Atari went with GEM instead. So there are roots both in CP/M and MS-DOS.
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