My contributions to the Boons/Hooks of the Covenant. Some of these are obvious, some are personal. All are free for discussion!
Boons
Vast and Labyrinthine: This makes sense if we are taking over the ruins of an old fort. It's entirely possible that we won't have explored the entirety of the ruins for some time...and it feeds into everyone having Dedicated Building for our labs.
Right: If we're given the land the Covenant sits on, it's entirely possible that we have been given the right to use some of the local baron's/lord's acreage for our use as well. I'd prefer this to be a forest, specifically for the use of lumberjacking. We are in a harbor, so we're going to need a navy at some point. So I want a shipyard. Sue me. 
Tame Nobleman: We're given enough land that we're going to end up controlling a town/village. According to the Order, magi cannot enter into feudal contracts, so we need a mundane figurehead. Someone who the local mundanes look up to and respect, but who is subservient to our "power behind the throne" rule, as it were.
Criminals: We're on a harbor, so the idea of having some former pirates around to help patrol and/or control our harbor sounds like a good idea to me. It also goes along with my wanting a shipyard.
Dedicated Covenant: For very obvious reasons. We've been tasked to do something.
Hooks
Road: If we are going to have a town/village that we are in control of, I think it makes sense that we might get some visitors from time to time.
Haunted: We are on the site of Roman ruins, and nobody really knows what happened to the ancient inhabitants. They might be a tad pissed off.
Contested Resource: I think this has been mentioned already, and I like stories about having to go out and actually acquire things we need.
Gender Imbalance: I think one of the topics has been about encouraging women to migrate to the town/village. Kind of makes sense that we'd have an imbalance here.