I am using Jabref--master--latest.jar (March 20, 2019).

I was missing the feature "find unlinked PDF files". I believe this already existed at some point but seems to be absent now. I use this feature often, and would like to have it back.

Since I am not using Java, in the meantime I wrote a simple BASH script. Maybe it can be used as a starting point?

#!/usr/bin/env bash

d="/path/to/papers/"
b="/path/to/library/library.bib"

cd "$d" || exit 1

while IFS= read -r -d '' file
do
    if ! grep -q "$file" "$b"
    then
        echo "$file was not found in bibliography."
    fi
done < <(find -- * -type f -name '*.pdf' -print0)

Thanks a lot for working on JabRef!