How do you batch decompile many class files?
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Take a look at Jode. You can disassemble .class files or complete .jars in one go. Although it claims to be up to date to an early version of Java (1.3), I've had few problems with later Java versions.
I've used JAD but I'm not sure if it supports the more recent changes (Update: it does not support language features introduced in java 1.5). Otherwise you might be able to write a small java app to do batch decompiling using the core of JD.
I just published a stand-alone Java Decompiler GUI (based on Jad) which you can get from Util Java Decompiler (JAD based) v1.0
This is a Windows based .NET 4.0 application, which supports the drag n'drop of *.jar files.
The code that creates that tool is a simple C# script (which you can see here: https://github.com/o2platform/O2.Platform.Scripts/tree/master/3rdParty/JAD ), so it would be easy to extend it to allow for the batch decompilation that you want to do.
It might be good to add support to the other Java decompilers, since JAD sometimes is not able to decompile some files.
JD-Gui makes your life easy, it also has an eclipse plugin