Also like, note: I would never publicly disclose whatever I find, I'm just curious

I observed exactly what you said about the Clojure filenames not matching up, etc. etc.

    #!/bin/bash
    
    # Variables
    DIR1=~/metabase-v0.46.6.jar.src # decompiled with jd-cli / jd-gui (java decompiler)
    DIR2=~/metabase-v0.46.6.1.jar.src # decompiled with jd-cli / jd-gui (java decompiler)
    
    # Function to create fuzzy hash for each file in a directory
    create_fuzzy_hashes() {
      dir=$1
      for file in $(find $dir -type f)
      do
        ssdeep -b $file >> ${dir}/hashes.txt
      done
    }
    
    # Create fuzzy hashes for each file in the directories
    create_fuzzy_hashes $DIR1
    create_fuzzy_hashes $DIR2
    
    # Compare the hashes
    ssdeep -k $DIR1/hashes.txt $DIR2/hashes.txt

I was thinking this, or binary diffing the .class (instead of the "decompiled" .java)?