Contiki/Makefile.contiki-top (PROJECTDIRS, CFLAGS): allow overriding of core/sys

We'll use this for a sanitized version of rtimer.h and rtimer.c
Shared/Contiki/Makefile.contiki (clean): invoke Contiki make with -i

This makes sure we clean up completely, even if there is a directory called
"core". This makes "rm -f" return an error which in turn causes make to
stop.