Tested QA cloudPush application using Jenkins ICEfaces EE 4 trunk Nightly build 433. Tested locally and on Labs1 server instance. I left the application running on Labs1 for Jack to view.
In the QA application I added the URI as per the new API. Now native notifications are no longer received and a server warning is seen when using priority push. This warning appeared with or without the modifications to web.xml.

Apr 06, 2016 7:56:43 PM org.icepush.ConfirmationTimeout execute
WARNING: Exception caught on confirmationTimeout TimerTask.
java.lang.UnsupportedOperationException
        at java.util.Collections$UnmodifiableMap.remove(Collections.java:1460)
        at org.icepush.ConfirmationTimeout.execute(ConfirmationTimeout.java:204)
        at org.icepush.ConfirmationTimeout.execute(ConfirmationTimeout.java:102)
        at org.icepush.ConfirmationTimeout$1.run(ConfirmationTimeout.java:56)
        at java.util.TimerThread.mainLoop(Timer.java:555)
        at java.util.TimerThread.run(Timer.java:505)

Also there was a server warning upon deployment. I ended up manually adding these Jackson jars to my .war file as they were not added during the build. I eventually commented out the email references in the web.xml file on the Labs 1 server.

Task.run E-mail Notification Provider is disabled by configuration.
Exception in thread "APNS Notification Provider set-up thread" java.lang.NoClass
DefFoundError: com/fasterxml/jackson/core/JsonGenerator
        at com.icesoft.notify.cloud.core.APNSNotificationProvider$AutoRegistrati
on$RegistrationTask.run(APNSNotificationProvider.java:445)
        at java.lang.Thread.run(Thread.java:745)
Caused by: java.lang.ClassNotFoundException: com.fasterxml.jackson.core.JsonGene
rator
        at org.apache.catalina.loader.WebappClassLoaderBase.loadClass(WebappClas
sLoaderBase.java:1295)
        at org.apache.catalina.loader.WebappClassLoaderBase.loadClass(WebappClas
sLoaderBase.java:1147)
        ... 2 more

The QA test app can be found at http://dev.icesoft.com/svn/repo/qa/trunk/Regression-Icefaces4/Sparkle/Manual/cloudPush.
Use the CloudPush Persistence page

Sending icepush/core/src/main/java/org/icepush/ConfirmationTimeout.java
Transmitting file data .
Committed revision 48616.

The UnsupportedOperationException should be fixed as instead of changing references of the propertyMap the class member propertyMap is now cleared and the parameter propertyMap is then added in its entirety to the class member propertyMap. As the class member propertyMap is under its own control and used by the execute(...) method the UnsupportedOperationException should no longer be thrown.

The targetURI is now part of the various public APIs, namely at the Java-side for ICEfaces (using the PushMessage class) and ICEpush (using the PushNotification class), and at the JavaScript-side for ICEpush (using the notify function). At the server-side the new targetURI eventually translates to the url property for the ICEnotify, ICEnotify-EE and/or Cloud Notification Service. Marking this one as FIXED.

EE4 trunk r45002, verified cloudPush priority notifications on Labs1 on iPad/IOS9:

• the UnspportedOperationException can no longer be reproduced. - VERIFIED/CONFIRMED.
• the notifications work partially only on iPad/iOS9. - NOTIFICATIONS WORK CONSISTENTLY; ONE EXCEPTION WOULD BE IF SENDING NOTIFICATIONS "IN A QUEUE" FROM DIFFERENT PAGES, WHEN ONLY THE FIRST NOTIFICATION IS RECEIVED.
• the notifications appear to work on iPad/iOS9 only if there is no other device that previously registered for cloudPush using the same application. If another device registered first for cloudPush from the same app, in order for the notifications to start working again on iPad, the browser on iPad should be cleared, and must register again for cloudPush from the iPad. - THIS WORKS CORRECTLY NOW.
• the received notifications contain the name of the color-coded page, and the subject line. - VERIFIED/PASS.
• clicking on the notification opens up the browser window displaying two tabs: the default opened tab is the second tab with the main registration page, and the first tab has the color-coded page that generated the notification. - this is expected and correct behavior – CLICKING ON THE NATIVE NOTIFICATION OPENS UP NOW ONLY THE CORRESPONDING COLOR-CODED PAGE.