The source code for the desktop & shell replacement got published by Gereon Steffens: https://github.com/gereons/gemini/ - the source represents a previously unpublished snapshot from mid 1991.
First forks appeared that got it compiled, e.g. from Thorsten Otto: https://github.com/th-otto/gemini
Gemini & Mupfel run on Atari TOS/MagiC/Geneva
I didn't know anything about this, but I found some English documentation here which explains it: http://www.atarimania.com/utility-atari-st-gemini_35572.html