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

This reverts commit 909e29be1117f9a82f145d85e36939d9f96004f2.

We now have the improved rtimers in our contiki tree, one step closer
to upstream.
Minor change to SAM4L_low_power_tick_management.c to ensure the alarm value cannot be set to zero.

git-svn-id: https://svn.code.sf.net/p/freertos/code/trunk@2120 1d2547de-c912-0410-9cb9-b8ca96c0e9e2
Merge remote-tracking branch 'trunk'