In the past, I've seen Sean Peyton and Drew Brees going over the gameplan for their upcoming opponents. Peyton would constantly ask Drew which plays he liked and was comfortable running in particular situations and then he'd incorporate them into the game plan for that week.
Just recently, while watching the NFL Network, I just saw a nice piece on Belichick. And I saw him and Brady doing the same thing with Brady telling him about a particular route and adding it to the plan.
Sincere question; I wonder if Harbaugh does that with Joe?