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!

doc/doxygen/Makefile

 RIOTBASE=$(shell git rev-parse --show-toplevel)
 # Generate list of quoted absolute include paths. Evaluated in riot.doxyfile.
 export STRIP_FROM_INC_PATH_LIST=$(shell \
-    git ls-tree -dr --full-tree --name-only HEAD |\
+    git ls-tree -dr --full-tree --name-only HEAD core drivers sys |\
     grep '/include$$' |\
     sed 's/.*/\"$(subst /,\/,${RIOTBASE})\/\0\"/')