It causes problems when different applets (or different classes used by different applets) are given the same name. Browsers and proxy servers can get confused. The recommended solution is to put your applets in different packages that are unique to your organisation and to exclude those package names from obfuscation.
If you then obfuscate the package as a whole, then each class will be given a unique name within the name space of the package. However, it is recognized that, for various reasons, not everyone wants to do this. The best alternative way of handling this situation is to use Zelix KlassMaster's Input Change Log functionality.
Perform a preliminary obfuscation with all of your applet classes opened inside Zelix KlassMaster. Don't bother saving the obfuscated classes. All you want is the "cross applet" change log with each class being given a unique name.
Now obfuscate each of the individual applets using the "cross applet" change log as an input change log so that each ... more.
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