Fix doxygen warnings on function signatures

src/include/file_io.h

src/include/sph_subs.h

src/include/tra_subs.h

src/libnptm/TransitionMatrix.cpp

src/libnptm/clu_subs.cpp

src/libnptm/sph_subs.cpp

src/libnptm/tra_subs.cpp

src/trapping/np_trapping.cpp