Don't close fds in write_init_super

Don't close fds in write_init_super

We previously closed all 'fds' associated with an array in
write_init_super .. sometimes, and sometimes at bad times.
This isn't neat and free_super is a better place to close them.

So make sure free_super always closes the fds that the metadata
manager kept hold of, and stop closing them in write_init_super.

Also add a few more calls to free_super to make sure they really do
get closed.

Reported-by: Adam Kwolek <adam.kwolek@intel.com>
Signed-off-by: NeilBrown <neilb@suse.de>