Merge pull request #3045 from RosettaCommons/aleaverfay/fix_jd3_out_path_all
output path handling for structures written by JD3
Pose outputters for JD3 now respect the -out::path, -out::path::all, and -out::path::pdb flags.
Addressing issue brought up by @BYachnin: https://github.com/RosettaCommons/main/issues/3034