Current source code and documentation of Fernflower is available here: https://github.com/fesh0r/fernflower

Command line options are listed there, I do not copy-paste them from github.

Online version of Fernflower is now available on this site: http://www.javadecompilers.com/

You can get it looking at JetBrains releases: https://www.jetbrains.com/intellij-repository/releases/

Download the java-decompiler-engine.jar which will actually have the version name, but for simplicity I'll save it as c:\t\dl\jde.jar on my pc.

Then this for example will decompile the jar file for the game Necesse where I have it installed on my PC. The output seems to go into a jar file with the same name in the directory specified, here creating c:\t\Necesse.jar with the .java files in it (command split into lines for readability):

java -cp c:\t\dl\jde.jar
  org.jetbrains.java.decompiler.main.decompiler.ConsoleDecompiler
  'c:\games\steam\steamapps\common\Necesse\Necesse.jar'
  c:\t