Reset the SAM3X8E before flashing
so as to avoid some hangups in the flashing process
sys/transcevier: fix more loop integers
vtimer: fix crash on spurious hwtimer callback

It seems that there are corner cases where a vtimer was removed, but
still there comes a hwtimer callback. This is a bug somewhere in the
vtimer or hwtimer. If there still was a vtimer set, then the next one
gets called before its time. If there was no other vtimer scheduled,
then `timer->action(timer)` crashes.

This PR simply fixes the crash, but does not attempt to find the more
fundamental bug.
Make filenames in periph documentation unique

This makes the filenames in the documentation of low-lever peripheral
drivers unique, so doxygen stops complaining about duplicates.
ccnl: use a second helper thread to handle e.g. timeouts
ccnl: use vtimer instead of rtc
ccnl: make theRelay use dynamic memory
ccnl: make relay start on RIOT startup
ccnl: use stacksize main for all threads
ccnl: prevent race condition on teardown
ccnl: adapt HOWTO to new features
ccnl: change timeouts to useful values
ccnl: normalize time before using it
ccnl: fix function name
ccnl: finish rebase
Merge pull request #1447 from authmillenon/periph-doc-fix

Make filenames in periph documentation unique
Merge pull request #1446 from Kijewski/vtimer-spurious-hwtimer-call

vtimer: fix crash on spurious hwtimer callback
examples: changed stacksize to the recommended value
Merge pull request #1320 from mehlis/ccnl-timeouts

ccnl: change timeouts to useful values
Merge pull request #1026 from mehlis/ccnl-helper-thread

ccnl: refactor ccn lite stack