I have recently written an obfuscator for JavaScript in Java. It is available at:
http://www.shaneng.net/
It exploit some feature of JavaScript so that I don't need to understand the content of JavaScript. To start, the obfuscator just "blindly" replace the variables without leading dot (e.g. window.parent has the dot). Then, I managed to remove the comments. Later, it also encode character in the string literals into \uXXXX or \XXX format.
In the current version, I refactor it so that it is more managable. In the future, I would like to handle the source code with E4X syntax.
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