[AVR32] Fix bogus ti->flags manipulation in debug handler

We should OR in a bitmask, not a bit offset, into ti->flags. This
might fix some strange behaviour when single stepping.

Also, use set_ti_thread_flag() to manipulate the flags to avoid
surprises in the future.

Signed-off-by: Haavard Skinnemoen <hskinnemoen@atmel.com>