fix file permissions

bioem.cpp

bioem_cuda.cu

cmodules/affinity.cpp

cmodules/affinity.h

cmodules/get_private_profile.h

cmodules/os_low_level_helper.h

cmodules/pthread_mutex_win32_wrapper.h

cmodules/qmalloc.cpp

cmodules/qmalloc.h

cmodules/qmultialloc.cpp

cmodules/qmultialloc.h

cmodules/sched_affinity_win32_wrapper.h

cmodules/switchtemplate.h

cmodules/threadserver.cpp

cmodules/threadserver.h

cmodules/timer.cpp

cmodules/timer.h

include/bioem.h

include/defs.h

include/map.h