Put a text document in this location named deployment.properties
Despite what Java documentation says, you do not need the deployment.config file unless you want to use the manditory setting.
This file will change the default for every user on the computer, even if they already have a deployment.properties file in their appdata folder. You can verify that the settings are taking effect when you open the java 32 control panel since it reads the settings then.
Here are some of the things we put in our deployment.properties file.
#disables the java desktop shortcut on install - might not be required for modern versions
#tells sets security level to it's minimum "MEDIUM" to allow for apps to run on outdated java versions
#disabled certificate checking so that java apps load much faster. Java still checks the certificate
#blacklist though so the certificate is still used.
#moves the user trusted certificates store to a shared location so we can pre-approve controls
The last bit is the best way to get rid of "do you want to run this app" boxes. Once you set the trusted.certs location to a shared location, create your own trusted.certs file by manually going to the process of checking the box "don't show this again". They deploy this trusted.certs file to all your machines with this deployment.properties file and viola, no more security pop-ups.
Note that the extra slashes in the path are required. Colons are reserved characters and the backslash is the escape character.