Not official clones, and I haven't tried them but they look good:
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I used to spend way too much time on Freeciv.
I wish there was some kind of open-source Total War.
I love openRA for dune and I love openRTC too.
Panzer General with lots of campaigns and quite deep gameplay, also runs in browser and on mobile
https://rayfowler.itch.io/remnants-of-the-precursors
Master of Orion fan remake
Xonotic doesn't really count, its mechanics are purposefully unique to itself but it keeps the Darkplaces engine going, you can play lots of wayyyy old quake maps and it is fun as hell.
I always loved the total annihilation clone made with springrts
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