Unreal World. Released in 1992. Though I didn’t first play until 2010ish when I moved to linux.

Cataclysm DDA. It’s a roguelike zombie survival game with an extensive crafting system. Not sure exactly if this meets your criteria, it has no new spawning zombies. You can kill all the zombies, but the city doesnt get repopulated with people.

In my current game i’ve nearly completely cleared the nearest city and have reclaimed a farmstead on the outskirts and installed solar panels and have livestock and vegetables planted.

cmus.

I know it satisfies 1, mostly sure it satisfies 2, and looks like 3 was implemented somewhat recently

https://github.com/cmus/cmus/pull/1325

yep, just tested and resume works.