kernel: streamline initialization of _thread_base and timeouts

Move _thread_base initialization to _init_thread_base(), remove mention
of "nano" in timeouts init and move timeout init to _init_thread_base().
Initialize all base fields via the _init_thread_base in semaphore groups
code.

Change-Id: I05b70b06261f4776bda6d67f358190428d4a954a
Signed-off-by: Benjamin Walsh <benjamin.walsh@windriver.com>