Merge pull request #3348 from RosettaCommons/aleaverfay/jd3_fix_score_file_in_jobdef
jd3 fix score file in jobdef
I discovered that a few things concerning how score file output is controlled in the job definition file for JD3 were not working correctly.
1. If a (non default) filename were provided inside the ScoreFile tag, it was not getting used.
2. If multiple ScoreFiles were listed in a single SecondaryOutput tag for a job (say you want to record the job's scores in two locations), then the schema validator would throw an error.
3. (related to 2.) The StandardJobQueen didn't really support the idea of allowing multiple SecondaryOutputters, so even when you fix the schema definition bug, there are other things lying in wait.
I've fixed these issues. Now you can say for job 1 that the outputs will go to directory1/ and for job 2 that the outputs will go to directory2/.