Renamed global index type to Index to avoid shadowing

api/legacy/include/gromacs/selection/indexutil.h

api/legacy/include/gromacs/topology/atoms.h

api/legacy/include/gromacs/topology/symtab.h

api/legacy/include/gromacs/utility/basedefinitions.h

api/legacy/include/gromacs/utility/listoflists.h

src/gromacs/applied_forces/awh/biassharing.cpp

src/gromacs/applied_forces/awh/biasstate.cpp

src/gromacs/applied_forces/awh/biaswriter.cpp

src/gromacs/applied_forces/awh/biaswriter.h

src/gromacs/applied_forces/awh/coordstate.cpp

src/gromacs/applied_forces/awh/correlationhistory.cpp

src/gromacs/applied_forces/awh/tests/biasstate.cpp

...d_forces/densityfitting/densityfittingamplitudelookup.cpp

.../applied_forces/densityfitting/densityfittingparameters.h

src/gromacs/applied_forces/qmmm/qmmmforceprovider.cpp

src/gromacs/applied_forces/qmmm/qmmmforceprovider.h

src/gromacs/applied_forces/qmmm/qmmmforceprovider_stub.cpp

src/gromacs/applied_forces/qmmm/qmmminputgenerator.cpp

src/gromacs/applied_forces/qmmm/qmmminputgenerator.h

src/gromacs/applied_forces/qmmm/qmmmoptions.cpp