doc: Only strip core, drivers, and sys include path prefixes

fixes tons of false warnings on cpu_conf.h headers in cpu

/tmp/RIOT/cpu/atmega1281/include/cpu_conf.h:12: warning: the name `/tmp/RIOT/cpu/atmega1281/include/cpu_conf.h' supplied as the second argument in the \file statement matches the following input files:
   /tmp/RIOT/cpu/atmega1281/include/cpu_conf.h
Please use a more specific name by including a (larger) part of the path!