SCHWED-1268: Use scoring module in overall pipeline.

doc/tests/scripts/loop_monte_carlo.py

doc/tests/scripts/modelling_close_small_deletions.py

doc/tests/scripts/modelling_fill_loops_by_database.py

doc/tests/scripts/modelling_fill_loops_by_monte_carlo.py

doc/tests/scripts/modelling_model_termini.py

doc/tests/scripts/modelling_steps.py

modelling/pymod/_closegaps.py

modelling/pymod/_pipeline.py

modelling/pymod/export_model.cc

modelling/src/model.cc

modelling/src/monte_carlo_scorer.hh

modelling/tests/test_close_gaps.py

modelling/tests/test_pipeline.py

scoring/pymod/export_backbone_score.cc

scoring/src/backbone_score_base.cc