Additional comments in cw.c, removing spectrum.py
Changed usart_test back to original version
Added doxygen comments to debug functions
Added doxygen comments to functions in manage.c
Added doxygen comments to nmea.c functions
Changed brackets of functions to Linux Kernel Coding Standard
Added doxygen comments to swift_nap_io.c
Merge remote-tracking branch 'fergus/master' into merge_fergus

Conflicts:
	src/manage.c
	src/swift_nap_io.c
Arguments to check_usart were swapped.
No writing partial messages unless we have support for writing rest
of message
Remove CW test
Broke up swift_nap_io into smaller submodules for groups of functionality
Changed acq_channel function and #define names
Moved STM on-chip peripherals to their own folder
Moved sources dealing with off-chip hardware into board/ folder
Moved nap/ folder to board/nap/
Changed include paths from previous few commits source path changes
Changed Doxyfile header
Adding submodules to manage module
Changed "debug" to "sbp" (Swift Binary Protocol)