Best way to decompile and analyze a large Java EE application (.ear / .jar)?

I have a local copy of a large enterprise Java application
(a .ear archive containing multiple .jar files, thousands
of .class files). I need to understand how a specific
part of the business logic works by reading the decompiled
source.

What's the best modern approach/toolchain for this in 2026?

- Which decompiler gives the most readable output for
large/complex codebases? (I've heard of JADX, Vineflower,
CFR, Procyon — which would you recommend?)
- Any good way to navigate and trace call flows across
thousands of classes once decompiled?
- Tips for dealing with obfuscated or hard-to-read
decompiled sections?

I have legitimate access to the software (it's for
interoperability analysis). Just looking for the most
efficient workflow. Thanks!