I don't think there are any free programs that allow you to do that. Albeit, it's a nice feature to have, but really not essential.
I will let you know though that Clip Studio Paint is currently on sale. I think the Pro version (cheaper than the EX version) allows for multi page story files and the like, so if you're willing to spend a little money, I'd highly recommend it, especially while it's on sale. EX is nice but Pro has everything you need.