The current code is a bit messy.
See the notes at https://github.com/windup/windup/wiki/Dev:-Decompiling .

https://bitbucket.org/mstrobel/procyon/wiki/Decompiler%20API
https://bitbucket.org/mstrobel/procyon/src/f496e46db5ce480700c89b41915a3f79c9055f3b/Procyon.CompilerTools/src/main/java/com/strobel/assembler/metadata/TypeReference.java?at=default

Decompiler API in general

3 main use cases: dir, .class, .jar

DecompilerConfig should also contain Filter<String> (or maybe Filter<TypeReference>) to decide whether to decompile the class or not.
windup.ProcyonConfiguration should extend abstract windup.DecompilerConfig, which would contain the configurables common to all decompilers. In case of Procyon, outputDir would be delegated to procyon.DecompilerSettings.

Procyon
Config

windup.ProcyonConfiguration contains procyon.DecompilerSettings.
procyon.DecompilerSettings contains outputDir (the others are not much important). TODO: Make that a parameter to method call?