updated Chronos support

All files, which used by chronos board were edited according to new texas instruments headers, all warnings fixed

* introduced variable for cpu folder

migrate native to current Makefile structure

set proper start of the stack in thread_stack_init for arm_common

* cleaned dist/Makefile up

stack_start used to be stack_start + stack_size, so re-setting stk to stack_start would set the pointer to the *end* of the stack instead of the beginning.

add Makefiles to sys/net

added and improved doxygen documentation

also fix and improve some of the existing

primitive native cpu target