Consistency update!

ADC.C and .H:
Several hardcoded values has been replaced with defines and the registers
are handled through a struct. Doxygen comments have been structured and
placed in header files. Inclusion prevention has been added and all
references to PMC has been removed (for modularity purposes).

TEST_ADC.C and .H:
Basic changes to reflect additions on src files. Nothing is tested yet. Do
not merge to integration branch before erevything is tested and
complete.
Smaller functions, less safety controls
First draft of refactored PMC (not tested)
First draft of refactored PMC (not tested)
Small fixes in ADC API

Small bug fixes within both adc.c & .h. The code passes all tests.
The functions are much smaller and performs a single repective task only,
with no safety checks for invalid parameters. New focus is that this check
is up to the programmer (the user of the API). Available macro for checking
valid channel ID's.
Cleaned unnecessary code in tests. They only perform and test a single task.
Removed init function in pio
Changed registers to struct in pio.h and changed all references to registers in pio.c and test_pio.c
Removed pio_close from pio.c and pio.h
Cleaned up the doxygen comments
Changed return in pio_read_pin from uint8 to uint32
Changed include to inttype.h in pio.h
CHanged brief descripttion of pio.h
were gonna use adc for test, not working
Test working, code working!

Bug with set_resolution was found and fixed. All previous tests are passed
and manual tests are passed. Still leaving commented code that needs to be
removed before final commit and merge.
Cleanup and final changes!

The init function now takes a struct as input parameter. The function checks
for illegal values returns error code if so. The code passes all tests, both manual
and automated, and the code is cleaned from comments.
Merge branch 'integration' into refactor-adc
merge with integration
Merge branch 'refactor_pmc' into refactor_API

Conflicts:
	src/sam3x8e/global_entities.c
	src/sam3x8e/global_entities.h
Refactored delay_soft

Delay_soft.h is now split up into a seperate .h and .c file, both called delay only.
Doxygen is changed to follow javadock standard and cleaned. The functions remain unchanged,
except for no longer being inline functions.
Merge branch 'refactor_delay' into refactor_API