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Try Running Command Line in Java Java jar files are the same format as zip files - so if you have a zip file utility that would let you modify an archive, you have your foot in the door.
Second problem is, if you want to recompile a class or something, you probably will just have to re-build the jar; but a text file or something (xml, for instance) should be easily enough modified.
That way you can just click on the ant file (if you use Eclipse) and rebuild the jar.
The reason i am interested in not un jarring is that the application is wrapped with launch4j if i unjar it i can't create the file again.
"Any files already in the archive having the same pathname as a file being added will be overwritten." See Updating a JAR File.
I think this answer would be a good answer to the question if you included some more of the details from your blog, within the answer itself so that someone reading your answer learns something even if they don't read the blog, or it gets moved to another URL at some future date.
In this command: The u option indicates that you want to update an existing JAR file.
Take a look at Packing Programs in JAR Files To clarify Null Pointer Exception's comment further: modifying a source file will have no impact on the related .class files and will therefore have no effect on how the jar file behaves when you run it (or compile with it).