logical diff:
core/include/hwtimer_arch.h
-has "hwtimer_arch_set_absolute"
-doxy is older
-header is older
core/include/arch/hwtimer_arch.h
-lacks "hwtimer_arch_set_absolute"
-doxy is better (but syntax broken?)
-header is up-to-date

Looks like one of them can go. The other one needs minor improvements.