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I thought the ST line was all about GEM.

If you're looking for an ST, they pop up from time to time on Goodwill's auction site.

I might be mistaken and it might be GEM. There was the base os and then another window manager it would go into.

I think you probably confused GEOS (C64 OS/GUI) with the Atari ST's GEM, GEMDOS, or GDOS. Lots of similar names!