I have a web app that has a portion of it functionality complemented by a native app. I have been using a URL Scheme to manage this, but with iOS 9 the user gets prompted with a Open In message that the users have been complaining about. Hooking up universal links seems to address this problem, but it introduces another.
I can get universal links to work from the Notes app, but I am unable to launch my native app from Safari unless I long press the link and select Open In <app name>. It seems a like a work around to this is to create a new domain that is only used to host the apple-app-site-association file. That way the web app and the native appss apple-app-site-association dont share the same domain. Am I missing someting? I'm not understanding why this would not be allowed.