Moved to new structure
Added root CMakeLists
Added src library CMakeLists.txt
Updated with GNU/Clang support
Added build directory to ignore list
Updated library naming scheme to be correct
Updated include paths to use new format
Added directory structure information
Removed obsolete 'make.sh'
Merge branch 'feature/Cmake' into NUClear
New directory tree markdown
Added pthread flag
Merge branch 'NUClear' into develop

Conflicts:
	include/NUClear/Reactor.h
	include/NUClear/ReactorController.h
	src/NUClear/Internal/CommandTypes.h
	src/NUClear/ThreadMaster.cpp
Cleaned up the moves