Refactoring utility::vector* classes to use platform SSize and Size instead of size_t and ssize_t. This should simplify PyRosetta cross compilation. Fixing some bugs in Windows build.

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Updates that implement stepwise monte carlo for proteins, on the way to unified SWM implementation for RNA/protein complexes (from rhiju/swm_general branch). Several additional fixes, including restoration of swa_rna_gagu_17 and swa_rna_gagu_20 integration tests, and addition of some swm_protein integration tests. Checked integration tests -- besides changes in RNA, SWA, and SWM tests, some cosmetic changes due to change in fa_standard patches and addition of TAUTOMER propery to HIS_D residue type. On my mac I also see a late change in an antibody test, which seems like a floating point deviation.

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Another bugfix for cryst docking

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updated default values for cb/n/o

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added interface_sigwidth option

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restoring graphics build after war(of the warnings) atrocity commited by sarel; also had an interrupted merge -- am trying to restore now.

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Removing some of "using namespace X" from headers. Fixing Windows build.

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added options to remodel, psipred prediction

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added options to remodel, psipred prediction

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Added options to Remodel, psipredfilter, per residue sasa

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Remove unused/meaningless version comments from fa_standard residue_types

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Remove a debugging line. Will fix the swa tests

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Bugfixes to cryst_design

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Fix swa_rna_main for terminal residues.

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adding an explicit flag to link to libstdc++. this seems totally gratuitous, I know, but for some reason is necessary on a cluster I have that just updated its gcc.

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Merge branch 'master' of github.com:RosettaCommons/main

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