md: separate flags for superblock changes

The mddev->flags are used for different purposes. There are a lot of
places we check/change the flags without masking unrelated flags, we
could check/change unrelated flags. These usage are most for superblock
write, so spearate superblock related flags. This should make the code
clearer and also fix real bugs.

Reviewed-by: NeilBrown <neilb@suse.com>
Signed-off-by: Shaohua Li <shli@fb.com>