We just did this....but we built UNDER a tree fort (fort is still without windows, as the boys don't wish windows! and the trim isn't yet on it in our photos)
We've left the bottom open to discourage anyone making a home there (huge groundhog population in neighborhood - if it's open, they won't come!) For winter use, I'll put straw bales completely around to help keep the cold out. And yes, do this late enough in the season, so that those same groundhogs will already have homes! Not to mention the chipmunks and the skunks and possums and and and!
We've built a portable pvc tractor as their run. It's got a port in the side so it will match up to their ramp - but so far, it's mostly stayed out in the grass with us transporting the chicks between the two on the few dry days we've had. Chicks are 6wks old, some pretty feather bare yet, so I"m concerned about keeping them healthy and dry and warm (which it's not been!).
We put hardware cloth completely around and underneath the siding and plywood floors (put the hardware cloth on first, then the flooring and siding) so the hardware cloth 'envelope' is complete from the base to the rafters. As the ceiling is the floor to the fort, we didn't hardware cloth there - it's a 1" plywood layer! Then put vents in the floor (vents from inside the coop to the inside of the tree fort) as well as two vents on the south side of the coop high on the walls. Vents are 4"x10" floor vents.
It's worked well - was fairly easy to 'remake' and while it seems like it took forever, what took forever was our sons helping with this project! But life lessons are lessons well worth the time. Always. Like growing chickens. Always.
Hope this helps.