Convert `use_fates_lupft` to an XML setting

> The `use_fates_lupft` option sets
>- `use_fates_luh`
>- `use_fates_nocomp`
>- `use_fates_fixedbiogeo`
>
>which is the primary scientific study for this work. This is settling a few things at once for convenience and also making it easier to do the primary setup.
>
>Because it's a conglomeration setting (turning several things on at once), longer term I think it should be moved into an XML setting. Technically it could also be in a build-namelist command line option or a use-case. But, we are deprecating those last two. Leave up to you if setting them all true, but leaving use_fates_lupft to FALSE is OK or not.
>
>Conglomeration settings should also check that the user isn't trying to set this on their own. So for example if the user try's to turn this on -- but turn one of these off individually that should fail.

_Originally posted by @ekluzek in https://github.com/ESCOMP/CTSM/pull/2507#discussion_r1659045690_