As of Java 7u45 an applet will display a warning message (even if signed with a trusted cert) if a webpage tries to interact with it via javascript and that page isn\'t list
EDIT: As it turns out, our app was doing something different if the file was in a different directory -- specifically, it wasn't attempting to access the applet signed jar manifests. So the fact that the file was in a different directory was irrelevant. So the below information is not accurate. I've decided to detail the real reason for the warning in a new question: As of Java 7 update 45, one can no longer lookup manifest information without triggering a warning?
Unfortunately, the workaround given by Oracle and others here for getting around the update 45 problem does NOT work if your app needs to access files in a different directory than where the app is being run from.
With my web start app, everything worked fine and dandy with the "Trusted-Library" attribute that needed to be added for 7u21. With 7u45, removing the "Trusted-Library" attribute and adding in all the additional attributes talked about in the other answers will NOT work -- I will get the same warning that you would get if you were running 7u21 without the Trusted-Library attribute (stating the application contains both signed and unsigned code).
It took me FOREVER to figure this out, because for very inexplicable reasons Oracle has decided not to print out ANY indication of what the "unsigned" code is in its console, even when running at maximum tracing (level 5). But basically, our app needs access to a configuration file which can be used by the user to configure application properties (for example, the logging level of our app). This configuration file is a plain old text file. And we store the config file in a directory co-located to where the app runs from: ..\config\app.properties. We access this file as a part of the main jar's init routine. It is here where the warning occurs.
The workaround here? Move app.properties into the same directory where the app is running from (and change the reference in the jar to just "app.properties"). Voila, it works -- no more warnings (as long as using the aforementioned codebase attributes). What the hell Oracle???
Unfortunately, because our app allows customized config files on a per-user basis, it is not as simple for us to just put the config file in the app's startup directory -- since that is NOT customized on a per-user basis, we would only be able to allow one user per machine to use the app simultaneously.
I've been looking over Java's manifest documentation to see if there is some way I can make the config file directory "safe" such that loading up of this file doesn't cause the warning. The only thing I can think of is either being able to use the Class-Path attribute or a combination of the Extension attributes (http://docs.oracle.com/javase/7/docs/technotes/guides/plugin/developer_guide/extensions.html), however these all seem designed around the purpose of jars, not just regular files...
Any ideas? And since Oracle intends to fix the Trusted-Library issue anyway, is coming up with a (potentially) grandiose workaround-solution around this even worth the effort? Grrr....