Is this by design? If so, is there an alternative aside from using the intransitive argument and hand picking everything (I’m worried about how we’ll be able to manage that given the number of conflicts we have)

Before answering your question, I have a few questions: 1. Why does the java_library exclude artifacts it looks like it has no (transitive) dependencies on? I just resolved org.apache.tikatika core1.3 locally an it pulls in 0 transitive deps. 2. Did you know jar(...) takes an excludes list to pinpoint excludes where needed?

Thanks John. RE 1. - I think that I screwed up the example. Let me go back and take another look. RE 2 - Based on this issue on Github (https://github.com/pantsbuild/pants/issues/4479), I thought that jar(...) didn't pay attention to excludes. Did that change?

It looks like the user from that issue was trying to exclude individual files from within a specific jar, not excluding some transitive dependency from the jar -- that functionality should work unless I'm misunderstanding you.