Merge pull request #5603 from RosettaCommons/jadolfbr/mrs_fixes
Fix some issues with MultistageRosettaScripts
This PR fixes the following.
- Enable MRS to actually work well with ParsedProtocol and control-flow.
- Enable MRS to not have a filter for every stage. If there is no filter, we add a TrueFilter.
- Disable all_results_are_not_in. This causes a lot of problems where the job just hangs.