Thank you again micuat. It’s working fine now! I think the issue may have been my incorrect ordering of the args to processing-java. As specified on GitHub, the args must be in a specific order, and paths given must be full paths. So, this works fine, and I see the Java generated:
processing-java --sketch=/Users/toby/Desktop/pj --output=/Users/toby/Desktop/pj/output --build
Thank you for your help!