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Summary:
Provide a descriptive summary of the issue.

Steps to Reproduce:
A native app is installed on the device that is programmed to be able to open a custom URL scheme.

Expected Results:
Clicking a URL scheme from a web page should open up the native app configured with the custom URL scheme.

We’ve tried several ways to use this custom URL scheme.
1. Using window.location: 
The javascript code looks like this:
window.location = ‘<custom-protocol>://XYZ’
 
2. Using an iFrame
The javascript code (using jQuery) looks like this:
$('<iframe/>')
.attr('src', '<custom-protocol>://XYZ')
.attr('style', 'display:none')
.appendTo('body'); 
 

Actual Results:
In iOS9 it won’t open the native app.

Regression:
Prior to iOS 9
1. Using window.location: This resulted in the native app showing up right away (no popups).
2. Using an iFrame: This resulted in the native app showing up right away (no popups).

In iOS 9:
 
1. Using window.location: This resulted in an alert popping up that asks a user whether they would like to open the app within the native app. The two buttons on the popup are “Open” & Cancel”. Tapping “Open” opens up the native app. Tapping “Cancel” dismisses the popup.
2. Using an iFrame: Nothing happens at all. No popups or app opening.
 
Notes:
1. Both approaches (window.location & iFrame) work when running within a Chrome browser on iOS 9, but with the same popup as mentioned above.
2. We’ve tried adding a whitelist (LSApplicationQueriesSchemes) within the app, but get the same behavior as described above for iOS 9.