This is a really good answer, but I've made an improvement (below) so that you don't need to create a new subdomain and you can just put *.domain.com in your entitlements, thus not relying on users/your own site from having to link to app.domain.com and allowing linking to domain.com and still have the deep links work. This is pretty important if you have users sharing links between web and mobile, and of course also if you just want clean and consistent domains across your web/mobile apps.