Removed some small and unhelpful classes

src/adjmat/ActionWithInputMatrix.cpp

src/adjmat/ActionWithInputMatrix.h

src/crystallization/BondOrientation.cpp

src/crystallization/InterMolecularTorsions.cpp

src/crystallization/MoleculeOrientation.cpp

src/crystallization/MoleculePlane.cpp

src/crystallization/OrientationSphere.cpp

src/crystallization/OrientationSphere.h

src/crystallization/VectorMultiColvar.cpp

src/crystallization/VectorMultiColvar.h

src/multicolvar/AlphaBeta.cpp

src/multicolvar/Angles.cpp

src/multicolvar/Bridge.cpp

src/multicolvar/BridgedMultiColvarFunction.cpp

src/multicolvar/BridgedMultiColvarFunction.h

src/multicolvar/CenterOfMultiColvar.cpp

src/multicolvar/Density.cpp

src/multicolvar/DihedralCorrelation.cpp

src/multicolvar/Distances.cpp

src/multicolvar/InPlaneDistances.cpp