I don\'t get applinks: in iOS not working, whenever I open a link like https://www.example.com/something on my iOS 9 device, it gets opened in Safari.
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I spent a good amount of time trying to fix this issue today. It finally came down to the setup of my SSL certificate. Things you should check for:
1) In the device console in XCode (Window - Devices, select your iphone, and open the dialog by clicking the triangle in the bottom left of the main view), do you see "Rejecting URL for auth method 'NSURLAuthenticationMethodServerTrust': kAuthenticationError"? If so, this means that your SSL certificate is most likely not properly setup.
Use https://cryptoreport.websecurity.symantec.com/checker/views/certCheck.jsp to make sure there are no SSL cert errors with your website.
Also if you were bypassing TLS 1.2 in your infoplist you may have to remove those keys as well.
2) Make sure to turn on Associated Domains at developer.apple.com for the correct App ID
3) Make sure to add the appropriate applinks to the Associated Domains within the Project Target of XCode. Also make sure the entitlements file got added to your project. I read somewhere that this file didn't get generated for someone and that may be your problem as well.