vtimer: fix usage in test application
core/hwtimer: disable interrupts in hwtimer_remove

Before only the hardware timer's own interrupt was being disabled.
This led to a race condition in the following scenario:

```
Thread1:
    hwtimer_remove()
    hwtimer_arch_disable_interrupt();

// INTERRUPT -> Thread2 (which has a higher priority than Thread1) gets scheduled

Thread2:
    ...
    hwtimer_remove()
    hwtimer_arch_disable_interrupt(); // hwtimer interrupt is already disabled
    ...
    hwtimer_arch_enable_interrupt();
    ...
   // yield | terminate -> Thread1 gets scheduled again

Thread1:
    ... // these instructions are being run with the hwtimer interrupt enabled
    hwtimer_arch_enable_interrupt(); // hwtimer interrupt is already enabled
```

Fixes #924
make: fix #1197

Partial revert of 85b7eca19edf76a5b82c2ebe01e0e90a3292dee7

Fixes #1197.
make: make clean usable together with `-j`
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.
unittests: support Makefile.include in test suites

This change will pull in the `Makefile.include` for every test suite
that is compiled in.

Fixes #1205.
Merge pull request #1000 from OlegHahm/prefix_core_api_functions

core: prefix API functions correctly
documentation: fix doxygen for `pthread_*.h`

The pthread header files aren't in the doxygen page anymore after #1137,
because I `@file`'d the `.c` files, not the `.h` files.

This change moves doxygen boilerplate.

Closes #1199.
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
msp430: workaround: define errno values if not provided by MSP430 lib