Use SuspendAllInternal for FlipThreadRoots

Fix FlipThreadRoots to wait until all the threads are suspended by
using SuspendAllInternal. Since running threads no longer hold the
mutator lock as shared held, doing an exclusive lock will not block
if the threads are not suspended. Also implemented MarkHeapReference
which is used to preserve soft references.

Fixes CC tests.

Change-Id: I4b059238f4249cf297e21ae918becd029fe26527