Fix swa_rna_erraser test.

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Fix element loading with ResourceManager. This should make the file_list_locator and residue_data_resource integration test work appropriately again. Also fix some database files which were missing the elements line.

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Fix the erraser_minimizer app. Fix a bug in ICY rna residue type.

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Updating benchmark/integration.py script so it remove all bin/* symlinks before building. This should prevent deleted executable from being reused in integration tests. Thanks to Rocco for suggesting this idea!

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Restoring correct functionality of core/scoring/sc/MolecularSurfaceCalculator::AddAtom on Windows platform. Fixing some compilation errors when compiling with MSVC.

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Updating PyMOL Mover. Adding pymol_name functions.

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sigwidth fix

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Exiting with exception now gives non-zero exit codes Change the standard try/catch block such that exceptions cause the program to exit with a non-zero exit code. As a consequence, (properly written) integration tests will now correctly show when program exits cleanly, or when it errors out. Update app_exception_handling to test that applications exit with non-zero error codes when passed bogus options. I somewhat arbitrarily picked "-1" as a general "something wrong's happening here, what it is ain't exactly clear" code. This can certainly be changed if anyone is so inclined. (One possibility is to embed the exit code to use in the exception itself, in case we want to use it to pass signals up the chain.) Also, fix some dos-mode line endings issues. ** Integration test changes expected: app_exception_handling - different command file. jrelax - was erroring out with a bad option. Now fixed. The following integration tests have errors, and should now continue to fail until those errors are fixed: swa_rna_gagu_20_append_floating_base_by_jump swa_rna_gagu_17_append_floating_base swa_rna_erraser erraser_minimize swm_nickedhelix

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Scoping to current class is apparently not uneccessary "Considered an error by many compilers", absolutely required by others

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[minor update of SandwichFeatures] - exclude H for number_of_RK_in_sw - default min_sheet_angle_by_four_term_cen_res (defined by 3 middle residues in each edge strand)= '25' since during repopulated de novo design of 3_1L9N, '27.2' of min_sheet_angle was observed for ideal-looking decoy - added a destructor - more int than Size to reduce Xcode warnings - restored accidently deleted 'do not face' phrases where appropriate [integration tests comment] - should not change other than features and features_database_schema (if any)

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Fix ccpcheck errors Ran cppcheck 1.49 on all *.cc and *.hh files in src/ using --suppress=stlOutOfBounds (as cppcheck is confused by vector1's) No test changes observed locally. Did not touch anything in src/apps/pilot, but addressed everything else: * Memory allocated with new[] needs to be freed with delete [] src/basic/gpu/GPU.cc src/core/io/serialization/serialize_pose.hh src/core/scoring/sc/ShapeComplementarityCalculator.cc src/numeric/geometry/hashing/xyzStripeHash.cc * Add freeing of memory in alternate code paths src/core/scoring/electron_density/ElectronDensity.cc * Address possible memory leak with realloc src/utility/libsvm/Svm.cc * Fix deletion from vector while iterating over it src/protocols/forge/build/SegmentInsert.cc src/protocols/forge/build/SegmentRebuild.cc * Fix use of the wrong object in iteration src/protocols/docking/DockingHighResLegacy.cc * Division by zero issues src/protocols/simple_moves/TailsScoreMover.cc * cppcheck says scoping to current class is "unnecessary and considered an error by many compilers" src/core/pack/interaction_graph/DoubleLazyInteractionGraph.hh src/core/pack/interaction_graph/LazyInteractionGraph.hh src/core/pack/interaction_graph/LinearMemoryInteractionGraph.hh src/python/bindings/src/utility/_utility__by_hand_beginning.cc * Spurious parenthesis and missing curly braces (some of these files might not be compiling) src/core/chemical/sdf/ctab_parser.cc src/devel/path_rover/pathrover.cc src/devel/path_rover/pathrover.hh src/devel/simple_options/test.hh src/devel/simple_options/working/test.hh src/protocols/noesy_assign/Assignment.hh src/protocols/noesy_assign/CyanaModule.cc * Random code that has been ifdef'ed out for over 6 years - I think it's safe to say we don't need it anymore src/protocols/jobdist/JobDistributors.cc

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Splice log changes. Expect log changes in splice integrations tests.

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ConstraintSetMover previously deleted the current constraints from the pose and imposed the newly read ones on it. This behaviour is sometimes undesired. I addd a flag, defaulting to false, named add_constraints, which instead of overriding the previous constraints adds new ones. See wiki for details; no test changes expected.

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merge onto a commit to fix layer design Merge branch 'master' of github.com:RosettaCommons/main

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Fix warnings issues seen on gcc4.4 but not gcc4.8

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Address debug mode integration failures. In which I promote assert()s to runtime_assert()s to make long-standing errors more noticable. Also, reenable compilation of an application that somehow got disabled. Integration test changes expected for those tests currently failing in debug mode.

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