The Atari ST's operating system ("TOS") was forked from Digital Research's 'GEMDOS' (a kind of CP/M 68k / MS-DOS alike disk operating system) along with 'GEM' (Graphic Environment Manager) which consisted of a device-independent graphics subsystem ('VDI') and a windowing system / application toolkit ('AES' application environment services). Atari was given a license from DR back in 1984, and effectively did their own port and forked from the mainline. The story of how that all went down is chronicled in an excellent series of blog posts by an original participant here: http://www.dadhacker.com/blog/?p=995 and http://www.dadhacker.com/blog/?p=1000
Note that this is 'Atari Corp', which was a company owned by Jack Tramiel after he quit Commodore. Not Atari Inc, which was the company responsible for Pong, the Atari 2600, and the original Atari 8-bit computers.
GEM was the brainchild of Lee Jay Lorenzen, who had worked on the Xerox Star project and who had advocated at Xerox for getting some of those concepts onto lower end PC-class machines. He joined DR in the early 80s and headed up the GEM project to work on that. He later left DR to start Ventura Publisher, an excellent DTP package which was built on GEM.
Digital Research went on to develop GEM on the x86 on a separate branch from the Atari version. They were forced by an Apple lawsuit to make modifications to it to make it less Mac-like. Atari's branch was exempted from this.
Atari Corp eventually packed it in, with their assets spread around like ashes, and the IP around their fork of GEM/GEMDOS has been lost to the world (well the source has been leaked but not legally). However after a series of acquisitions, DR's original IP -- including GEM, GEMDOS, CP/M 68k, etc. was open sourced under the GPL.
EmuTOS was created (many moons ago) from the original DR sources in order to have open source ROMs for ST emulators, effectively doing again what the team at Atari did back in the 80s: porting to the 68k Atari ST platform. But since then it's grown to be a full alternative to Atari's ROMs that works on more than just emulators.
In addition to being basically full feature (and quirk) parity with Atari's TOS, it also includes a full hard disk driver which is something Atari's never included without an add-on. This includes support for IDE drives for modern devices like compact flash cards, etc.
It also has been ported to and runs well on other 68k and Coldfire platforms, and runs well on the Amiga, on the Firebee (a modern Coldfire based Atari-like machine), and headless on Coldfire evaluation boards. It's also been recently ported to the 'Kiwi' 68008 DIY microcomputer.
I don't remember having to do anything to use a hard disk with any of the official versions of TOS.
I have an SH204 "shoebox" HD from the initial developer offer.
Usually ICD, AHDI, or HDdriver (still maintained).
Here Lee Jay Lorenzen is showing off his prototype while at Xerox in 1982, before he joined Digital Research. Before the Lisa or Macintosh were released:
Think of an Atari ST as a Commodore 64 (Tramiels and Shiraz Shivji worked on both) in a roadside collision with a Macintosh (GUI) and CP/M machine (GEMDOS).
JACK ATTACK: The Story of Jack Tramiel at Commodore, Part 1 - Kim Justice
Jack Tramiel Part 2: The Commodore 64 vs The TI-99/4A and the American Computer Crash - Kim Justice
The Last Stand of Jack Tramiel: The Atari ST vs The Commodore Amiga - Kim Justice