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
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. :)
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.
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
Merge pull request #1189 from Kijewski/compile_test-empty-folders

buildtest: ignore empty folders
native: set _native_pid correctly in daemon mode

This fixes a bug that leads to all unix sockets being created as
`/tmp/riot.tty.0`.
Merge pull request #1213 from OlegHahm/ubuntu_msp430_errno_fix

msp430: workaround: define errno values if not provided by MSP430 lib
Merge pull request #1216 from LudwigOrtmann/issue-1215

native: set _native_pid correctly in daemon mode
Merge pull request #1208 from Kijewski/issue-1199

documentation: fix doxygen for `pthread_*.h`
core: kernel: improved doxygen documentation

also added param[in] to irq.h and fix order of doxygen endguards
Merge pull request #977 from mehlis/doxygen-irq

core: kernel: improved doxygen documentation
Merge pull request #1193 from LudwigOrtmann/issue-924

core/hwtimer: disable interrupts in hwtimer_remove
Complete the definition of low-level radio driver API
Merge pull request #1211 from rousselk/complete-radio_driver_h

Completing low-level radio driver definition.
documentation: CMSIS cleanup

Put all CMSIS documentation into a dedicated subgroup of cpu.
documentation: moved network documentation to top level
documentation: added missing doxygen header to transceiver interface
documentation: fixed organization of 6LoWPAN doxygen