Adding pilot apps to pilot/nmarze. Nothing used by unit/integration tests was changed.

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PyRosetta, debug build: Adding link to toolbox.

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fixing broken pyrosetta build

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Commenting out guilty methods for breaking pyrosetta build - hopefully we fix it this time'

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merging (small) changes with the current state of the trunk

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Updating include guards again. HOpefully this fixes the pyrosetta build

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Updating include guards in Membrane FA Potential class. THis should hopefully fix the pyrosetta build

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Added a new mover (ResidueTypeConstraintMover) that assigns a ResidueTypeConstraint to a pose (All I did is just making a simple mover using Sarel's ResidueTypeConstraint) [integration tests comment] - should not change any integration test

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Fix low-hanging gotos Fix gotos that were simple replacements of break/continue/do-while/etc. The gotos that are remaining are either multi-level breaks, other more complex flow control, or in files I didn't bother to touch. (I didn't bother with the multitude in apps/pilot/, as many of those are in "private" applications, and some numeric/ files, as those look to be straight transliterations of external code.) All tests pass on my machine.

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A simple pilot app demonstrates how to use movers

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fixing warning/error which should also fix the build

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a pilot app reads a binary PsiBlast ckeckpoint to test the new functionality

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Fixing the build on Mac with clang >= 5.0 It compiles nicely by clang 5.0 and gcc.

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Fixing unittest for mac build, lower tolerence

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Updating Centroid Rotamer (cenrot) Model 1. reweight pair and pair_ang by env dependency 2. refined rotamer cluster, new cenrot dunbrack lib 3. cbeta term for cenrot 4. bigger vdw radii for minimizing 5. updating unit test 6. minor bug fixing for compiling others: Adding more parameters for cart_bonded term Hack in CartesianMinimizerMap, use RB1 to mark single atom vdw term can load more than one atom_vdw.txt Unit test all passed 53 ingegration test changes found 12 of them due to the cart_bonded term or new cenrot weights file FAIL nonideal_rtmin FAIL mr_protocols FAIL hybridization FAIL fold_cst_new FAIL metalloprotein_abrelax FAIL abinitio FAIL splice_seq_constraint FAIL repack_with_elec_dens FAIL minimize_with_elec_dens FAIL features_database_schema FAIL symmetry_multicomponent 2 of them just failed as ref (missing weights file?) FAIL splice_out FAIL splice_in others are minor numeric changes due to adding new cenrot_cbeta term

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Removing erroneously typed character to fix the build

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