Make an initialization pass for the thread context and set the [phys,virt]Port correctly

Make an initialization pass for the thread context and set the [phys,virt]Port correctly

src/cpu/simple/atomic.cc:
src/cpu/simple/timing.cc:
    Call the thread context initialization

--HG--
extra : convert_revision : d7dc2a8b893dc670077b7f6150d4b710a1778620