make: fix #1197

Partial revert of 85b7eca19edf76a5b82c2ebe01e0e90a3292dee7

Fixes #1197.
documentation: clean up doxygen mess after cortex

fixes #1190
Merge pull request #1194 from LudwigOrtmann/cortexygen

documentation: fix generation Doxygen documentation after Cortex import
Merge pull request #1198 from Kijewski/issue-1197

make: fix rebuilding on changes without `clean` or `-B`
tests: added a thread_sleep() at the end

Letting the main thread exit could cause failing test if thread_exit()
is broken for the tested platform, preventing the actual testing of the
hwtimer.
Merge pull request #1083 from OlegHahm/test_hwtimer_w_thread_sleep

tests: added a thread_sleep() at the end
core: prefix API functions correctly

Also changed names for bitarithm functions and rename thread_pid to sched_active_pid.
Merge pull request #1000 from OlegHahm/prefix_core_api_functions

core: prefix API functions correctly
documentation: fix CMSIS doxygen for SAM3x8e
documentation: fix doxygen group for Z1
Merge pull request #1202 from OlegHahm/cortex_doxygen_cleanup

documentation: cleanup doxygen for SAM3x8e and Z1
Fix application name for test_bloom_byte application
Merge pull request #1212 from authmillenon/fix-application-names

Fix application name for test_bloom_byte application