1. Trees, Ores, and Bushes can spawn in the same square as the buttons that you have to hit with your hammer, but you cannot manually harvest them in any way. You can however build a mining turret thing in range, and they will happily harvest whatever grows on the buttons.
2. Select to build something (doesnt matter what) and then hover it over some water squares. Then press Esc. You can now walk over the squares of water you had the building hover over. You can also build on those squares.
3. After a while (I'm not sure exactly what caused this) I could no longer pick up any new items that I did not already have some of in my inventory. They just dissapeared. I did notice however, that I had a few unstacking items show up in my inventory that I just could not get rid of.
This is a very fun little game, and I eagerly await the next update. Keep up the good work!