Mark3 RTOS Source

Adding Source for Mark3 Kernel Configuartor utility

-Fixed up sanity test (works with mega644 and larger)
-Setting optimizations by default on 644s
-Updating build.mak to manage CPU-specific headers

Updated size_profile.sh to support multiple targets

Adding preliminary (And untested) ST7735 driver based on Adafruit implementation (heavily modified, with attributions in place)

Optimization and documentation updates:
- Removing dependency of BlockingObjects on Atomic functionality
- Making Atomic functionality a build option
- Moving a number of module-based defines into the global config file
- Updated docs for a few modules
- Fixed a couple of invalid mark3cfg.h combinations
- Adding a size-based profiling tool
- Adding size-based profiling output to the doxygen docs
- Rebuilt doxygen docs

Minor cleanup.

Minor refactoring, eliminating unnecessary CS_ENTER/EXIT's and simplifying some logic in ksemaphore.cpp

Creative-casting to fix build errors on SAMD20

Updating includes in atomic.cpp

Adding comments for atomic class