Update .gitignore

Same .gitignore as in integration. Now ignores .doxyfile
Updated gitignore
Merge branch 'release1'
FreeRTOS without any errors; not tested yet
Added threads; check description

vApplicationMallocFailedHook() will only be called if
configUSE_MALLOC_FAILED_HOOK is set to 1 in FreeRTOSConfig.h.  It is a
hook
function that will get called if a call to pvPortMalloc() fails.
pvPortMalloc() is called internally by the kernel whenever a task,
queue,
timer or semaphore is created.  It is also called by various parts of
the
demo application.

GETTING THIS ERROR
Added debugging using uart for rtos
Removed uneccessary files from rtos
Added twi header and source files. Added register mapping in the header file.
Merge branch 'twi' into integration
first draft
resolve conflict
resolved conflicts
Unity Hardware Setup has been cleaned!
Merge branch 'pmc_extension' into integration
fixed a bug in pmc_read_pin()
fixed bug in pio_set_port()
First draft of header file!

Created headerfile tc.h with initial struct of register mappings and doxygen comments.
Added draft of most basic functions!

Added definitions of basic functions like start/stop and
enable/disable clocks for each channel. Also for reading
counter values.
Added testing functions in main for RTOS
Changed RTOS Config (CPU_HZ)