lib: Add the exclude flag to notmuch_query_search_threads

Add the NOTMUCH_MESSAGE_FLAG_EXCLUDED flag to
notmuch_query_search_threads. Implemented by inspecting the tags
directly in _notmuch_thread_create/_thread_add_message rather than as
a Xapian query for speed reasons.

Note notmuch_thread_get_matched_messages now returns the number of
non-excluded matching messages. This API is not totally desirable but
fixing it means breaking binary compatibility so we delay that.