native: add missing include

crash.c was missing native_internal.h
Merge pull request #1196 from LudwigOrtmann/native_missing_include

native: add missing include
make: fix #1197

Partial revert of 85b7eca19edf76a5b82c2ebe01e0e90a3292dee7

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

fixes #1190
buildtest: ignore empty folders

`compile_test.py` fails if there are empty folders in `/examples` or
`tests`. This is not a problem for Travis, because it always has a clean
repo.

For the average users there is a problem if they work on multiple
branches and one branch has new examples or tests. If they don't delete
the residual `bin` folders, then `compile_test.py` will print out these
applications as having failed.

This change checks for the existence of a `Makefile` in the application
folder. Also I added a progress indicator, because I like it. :)
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
Merge pull request #1189 from Kijewski/compile_test-empty-folders

buildtest: ignore empty folders