I took a look at your city and for one you'll get space back when you sell the Dwarven settlement once you're done with the chapter (wait to get a quest asking you to sell the portal before selling it, I think you'll get 200 diamonds that way)
And then I see you have all the manus both of your boosted and not boosted goods. That's a huge wast of space. Your boosted goods are planks, scrolls and dust. At your current chapter you should only have those manus. You won't need the other manus until you get to chapter 12 and start producing sentient goods. And even then you won't need as many as you have so feel free to sell them. You'll get a lot of space and population back. Having manus of non boosted goods is never useful as you'll never produce enough goods with them. What you do is just concentrated to make a lot of your boosted goods and then trade for the rest.