OS X apparently doesn't support `System.setProperty("apple.laf.useScreenMenuBar", "true");` these days, so that line should be removed from the main method on PDFDebugger. The debugger app is a lot more useful with the menu than without. Forcing it to a single value in main disallows overriding it via `-Dapple.laf.useScreenMenuBar=false`, which means the menubar is invisible and unrecoverable in Mac OS X.
I built from source at HEAD on trunk, and run with the following command:
java -jar ./app/target/pdfbox-app-2.1.0-SNAPSHOT.jar PDFDebugger my-doc.pdf
After removing the aforementioned line and rebuilding, I have access to the menubar (which is handy!).