Merge pull request #2933 from RosettaCommons/sboyken/hbnet_interface_updates Updates to HBNetStapleInterface; a couple of fixes and new options for logic used when combining multiple networks together onto a single output pose

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Merge pull request #2940 from RosettaCommons/jaumebonet/FFLfixubsan FFL fix integration.ubsan

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Merge pull request #2938 from RosettaCommons/JackMaguire/MultistageRosettaScripts Small feature additions and bug fixes for multistage rosetta scripts: Features: - [x] Reverse script converter: convert a MRS script to a traditional rosetta script. Code is written but untested. - [x] Added a more dynamic result-storing method in the NodeManager class. Not super useful now, but will be essential when (if) JD3 is able to submit jobs from node n+1 before node n is completely finished. - [x] Added support for `<Checkpoint/>` tags to be intermixed with the `<Stage/>` tags. These do not currently do anything, but will save us time in the future. Bug Fixes: - [x] Each `<Add/>` call used to create a new mover/filter. This prevented us from being able to call the same mover twice (unfortunate for things like SaveAndRetrieveSidechains). Now, movers and filters can be called multiple times within the same MRSJob. I am taking this opportunity to remove the `job_bundle` Stage option because it is not that useful and really makes the code ugly. ~Upgrade the newick tree printing so that the values for the leaf nodes match the filenames created.~ - [x] Renumber the output files so that they match the newick tree

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Merge pull request #2922 from RosettaCommons/havranek/SASAFix Bug fixes for power diagram version of SASA calculations.

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beautifying

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Merge pull request #2924 from CyrusBiotechnology/for_commons/indigo/nmer_refactor NMerSVMEnergy core::Size underrun bug (from Cyrus) Fixes the addsan and numerical instability bugs in NMerSVMEnergy exposed by its new test. shoutouts to @indigogo and @vmullig for commentary and assistance shoutouts to @roccomoretti and @jaumebonet for notification.

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Merge pull request #2937 from RosettaCommons/jaumebonet/FFL2PyMOL Fixes NubInitioMover so that PyMOL observer does not get unlinked.

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RosettaAI: Setting rosetta_scripts_scripts submodule to latest origin/master version.

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Merge pull request #2932 from RosettaCommons/sergey/f fixing unit tests scripts used in academic releases

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Merge pull request #2865 from RosettaCommons/kalekundert/comments Add doxygen documentation for LoopHash.

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Merge pull request #2928 from RosettaCommons/tjbrunette/link_res_fix fixed possu's issue with template_res the issues with the testing server seem unrelated

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Merge pull request #2930 from RosettaCommons/sergey/ui-multi-jobs UI, adding support for multi-stage tasks

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Merge pull request #2915 from RosettaCommons/yhsia/SSElementSele_end_option fixing some issues with SSElementSelector & mergepdbmover

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Merge pull request #2929 from RosettaCommons/jaumebonet/dsspremark WriteSSEMover -> add dssp and/or psipred as a comment to the output

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Merge pull request #2926 from RosettaCommons/yhsia/quasi-flag_fixes code duplication fix in RotamerSets.cc

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Merge pull request #2921 from RosettaCommons/FFL_integration Adding integration test for FFL and correcting the errors of the valgrid and ubsan of the FFL unit tests

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