shell: print command if not found
shell: fixup test_shell expect scripts
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.
make: add comprehensive `buildinfo` list

Sometimes it is difficult to track down build errors for boards that you
are unfamiliar with.

This change adds `make buildinfo` that prints out all the relevant build
information for the selected board and project:

```
PROJECT: default
BOARD:   msba2
CPU:     lpc2387
MCU:     lpc2387

RIOTBASE:  /home/kijewski/RIOT/RIOT
RIOTBOARD: /home/kijewski/RIOT/RIOT/boards
RIOTCPU:   /home/kijewski/RIOT/RIOT/cpu

DEFAULT_MODULE: auto_init core cpu sys
DISABLE_MODULE:
USEMODULE:      arm_common cc110x_ng cc110x_spi config defaulttransceiver gpioint lib lpc_common ltc4150 mci net_help posix protocol_multiplex ps random rtc shell shell_commands sht11 timex transceiver uart0 vtimer

ELFFILE: /home/kijewski/RIOT/RIOT/examples/default/bin/msba2/default.elf
HEXFILE: /home/kijewski/RIOT/RIOT/examples/default/bin/msba2/default.hex

CC: arm-none-eabi-gcc
CFLAGSS:
        -DBOARD_MSBA2
        -DCPU_LPC2387
        -DMODULE_ARM_COMMON
        -DMODULE_AUTO_INIT
        -DMODULE_CC110X_NG
        -DMODULE_CC110X_SPI
        -DMODULE_CONFIG
        -DMODULE_CORE
        -DMODULE_CPU
        -DMODULE_DEFAULTTRANSCEIVER
        -DMODULE_GPIOINT
        -DMODULE_LIB
        -DMODULE_LPC_COMMON
        -DMODULE_LTC4150
        -DMODULE_MCI
        -DMODULE_NET_HELP
        -DMODULE_POSIX
        -DMODULE_PROTOCOL_MULTIPLEX
        -DMODULE_PS
        -DMODULE_RANDOM
        -DMODULE_RTC
        -DMODULE_SHELL
        -DMODULE_SHELL_COMMANDS
        -DMODULE_SHT11
        -DMODULE_SYS
        -DMODULE_TIMEX
        -DMODULE_TRANSCEIVER
        -DMODULE_UART0
        -DMODULE_VTIMER
        -O2
        -Wall
        -Wstrict-prototypes
        -mcpu=arm7tdmi-s
        -gdwarf-2
        -std=gnu99
        -fno-delete-null-pointer-checks
        -Wstrict-prototypes
        -Werror=strict-prototypes
        -Wold-style-definition
        -Werror=old-style-definition

LINK: arm-none-eabi-gcc
LINKFLAGS:
        -gdwarf-2
        -mcpu=arm7tdmi-s
        -static
        -lgcc
        -nostartfiles
        -T/home/kijewski/RIOT/RIOT/cpu/lpc2387/linkerscript.x

OBJCOPY: arm-none-eabi-objcopy
OFLAGS:  -O ihex

FLASHER: lpc2k_pgm
FFLAGS:  /dev/ttyUSB0 /home/kijewski/RIOT/RIOT/examples/default/bin/msba2/default.hex

TERMPROG: /home/kijewski/RIOT/RIOT/dist/tools/pyterm/pyterm.py
PORT:     /dev/ttyUSB0

DEBUGGER:
DEBUGGER_FLAGS:

MAKEFILE_LIST:
        /home/kijewski/RIOT/RIOT/examples/default/Makefile
        /home/kijewski/RIOT/RIOT/Makefile.include
        /home/kijewski/RIOT/RIOT/Makefile.modules
        /home/kijewski/RIOT/RIOT/Makefile.pseudomodules
        /home/kijewski/RIOT/RIOT/Makefile.defaultmodules
        /home/kijewski/RIOT/RIOT/boards/msba2/Makefile.include
        /home/kijewski/RIOT/RIOT/boards/msba2-common/Makefile.include
        /home/kijewski/RIOT/RIOT/boards/msba2-common/Makefile.dep
        /home/kijewski/RIOT/RIOT/cpu/lpc2387/Makefile.include
        /home/kijewski/RIOT/RIOT/cpu/arm_common/Makefile.include
        /home/kijewski/RIOT/RIOT/cpu/lpc_common/Makefile.include
        /home/kijewski/RIOT/RIOT/Makefile.dep
        /home/kijewski/RIOT/RIOT/Makefile.cflags
        /home/kijewski/RIOT/RIOT/sys/Makefile.include
        /home/kijewski/RIOT/RIOT/drivers/Makefile.include
        /home/kijewski/RIOT/RIOT/Makefile.buildtests
```
pkg/oonf_api: fix conflicting types on msba2
documentation: fix CMSIS doxygen for SAM3x8e
documentation: fix doxygen group for Z1