Begin renamind classes and putting them into namespace sot.

include/sot-core/additional-functions.h

include/sot-core/binary-op.h

include/sot-core/constraint.h

include/sot-core/contiifstream.h

include/sot-core/debug.h

include/sot-core/integrator-abstract.h

include/sot-core/op-point-modifier.h

include/sot-core/rotation-simple.h

include/sot-core/solver-hierarchical-inequalities.h

include/sot-core/sot-qr.h

include/sot-core/sot.h

src/debug/contiifstream.cpp

src/debug/debug.cpp

src/exception/exception-abstract.cpp

src/exception/exception-factory.cpp

src/factory/additional-functions.cpp

src/factory/command/import.cpp

src/factory/factory.cpp

src/factory/pool.cpp

src/feature/feature-1d.cpp