Yes, it is confusing. But the point is, we are tantalizing close to having something testable for you all. It won't be integrated fully and there may be a few caveats, but we need testing, and you need content. This is no coincidence. :D
In a day or two we will be uploading to the beta branch a newer version that will contain most of the new elements that will be fully integrated in the full alpha, which itself is not too much further out.
It probably won't have integrated saves, and you may need to just manually activate the mid-game until the transitions are totally coded in, but you'll be able to test out some of the new material a little bit ahead of time, if that's what you're into.
If not, just wait a few more days and we should have a stable, integrated build. But for those that want to get in on balancing and bug testing ASAP, this should suit you.
If you're not familiar with how to run the "beta" version, it's under launch options accessed from right-clicking FreeHolder in your library list. I will tell you as soon as it's available, and also any special steps to activate mid-game within the beta.
Thanks everyone!