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Unfortunately i dont think its possible.
You'd think a deployment could restrict warnings for a local intranet, or have an exception list.
There was another answer i did see but i would not recommend this at all. Even the person who put the post up does not recommend it.
You have two options, do not have java 1.6 on the desktop as this is the version that brings up the security warning. Or you can try the new
application with java 1.6 (As long as all functionality is tested). This will satisfy your new app, but not the applications that run of the older
java runtime environments. (we are going to test the application under 1.6 even though its not a supported certification by the vendor.)