bootctl: deprecate --make-machine-id-directory=auto

Now that kernel-install creates the machine-id directory, we don't need to do
this is 'bootctl install', and in fact it's better not to do this since it
might never be necessary. So let's change the default behaviour to 'no'.

I kept support for 'auto' to maintain backwards compatibility, even though the
default was changed. Previous behaviour can be requested by specifying
--make-machine-id-directory=auto.