Enigma is "a tool for deobfuscation of Java bytecode" : you can use it to edit method or class names inside a .jar file.
Enigma was originally a project from Cuchaz Interactive. It was meant to help reverse engineer Minecraft jar binaries.
I have decided to fork it because it had a NULL-pointer exception bug when handling certain functions (a critical one in my case...), and also the gradle dependencies were not up to date. The original README is kept intact in this repository.
In order to build Enigma, you need to have OpenJDK development tools and gradle installed.
gradle clean
gradle build
gradle jar
Build files are located in build/libs/. enigma-0.10.4b-all.jar is the one you are looking for :-)