shell: Add doxygen

Closes #577.
Merge pull request #1037 from Kijewski/issue-577

shell: Add doxygen
ccnl: use a second helper thread to handle e.g. timeouts
ccnl: use vtimer instead of rtc
import chunks fitting for MSBA2
don't include transceiver and defaulttransceiver
make theRelay use dynamic memory
appserver: remove unused flag
make debug easier
make relay start on RIOT startup
remove useless config module
don't include c files