Decompile Entire .Jar File (NOT Just .Java Files)?

[Aldraxic]

Currently, it only seems to copy .java files to the specified directory on decompilation, all other non-source related files aren't included through the compilation process.. Am I doing something improperly? I've checked the args/Wiki for more information, but it doesn't make things any clearer. What might I be missing? Thanks for the help. Note: I've also downloaded the decompiler from both the Releases page and also manually built the .jar with same results.