Watchdog is a Ultrastudio.org process that checks contribution for very strange-looking, potentially unfriendly code.
Watchdog is near full blown Java 1.5 compiler that performs checks if potentially controversal classes and methods are called. It uses the database where every method of every Java 1.5 class is described as either safe to call or potentially problematic if called from unfriendly code. Methods with the same name but different parameters are different methods and have different entries in this database.
Watchdog has no decision right by itself. Instead, its messages are checked by human operators before approving the committed code even for the test runs. This allow to lower threshold of alerts and also you do not need to check Watchdog conformance of your code; if the human sees that the code is fair it will be approved. However for such cases the reviewer must fully understand the part of the algorithm where the warning has been raised. If this is too difficult, the code is rejected also for obfuscation.
To make both reviews and watchdog efficient, the applets are not allowed to have sections that "would never execute in an applet" (logging, debugging, standalone run or similar statements). If found, such code is either simply removed or in some rare cases may be commented out.
When annotating classes, we mostly tried to be consistent with applet requirements: as unsigned applet should not even try to access file system or replace a classloader, such activities raise a warning that will be seen on a review. There is currently no big need for an Ultrastudio.org applet to open browser windows or contact our server on its own even if allowed on the client side. These and similar methods are also marked as 'questionable'.
Watchdog only looks into the code that Applet builder successfully builds first.