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Please see the original post here.
Changelog may be found here.
This release includes some bugfixes and balance fixes, as well as episode 5 of the Fallen Spire story campaign. The Fallen Spire story is really coming together at this stage, and this also has a lot of refinements to the prior episodes.
Also of significance is that the model for how big waves are has been completely redone. Fear the high AI Progress -- for real this time. In general this is attempting to bring back some of that "high AI Progress is super bad" flavor from AI War 2.0 and prior, while removing the insane difficulty of the earliest waves in the last few betas.
This is a standard update that you can download through the in-game updater itself, if you already have 4.000 or later. When you launch the game, you'll see the notice of the update having been found if you're connected to the Internet at the time. If you don't have 4.000 or later, you can download that here.