MINOR: thread: only use atomic ops to touch the flags

MINOR: thread: only use atomic ops to touch the flags

The thread flags are touched a little bit by other threads, e.g. the STUCK
flag may be set by other ones, and they're watched a little bit. As such
we need to use atomic ops only to manipulate them. Most places were already
using them, but here we generalize the practice. Only ha_thread_dump() does
not change because it's run under isolation.