The $site_id is part of what generates your session tokens - an internal security mechanism used predominantly in the manager (aka modauth), though that could potentialy also be used in front-end scenarios with logged-in users.
I don’t think $site_sessionname is in use. That may have predated the session_name system setting.
The $uuid is supposed to be a globally unique identifier for the MODX site. It is passed to package providers which could in theory use it for licensing or other sorts of tracking. I don’t think any public package providers rely on that, though.
Letting new values be generated for them, especially the site_id, would be recommended but it’s not an immediate problem if they’re reused on a cloned site.
Yeah typically they’re generated for you during the setup. I’m not 100% sure it’ll change them after running setup on a cloned site, though. I think it’s meant to keep them constant for a given site.
Running setup after a migration or clone is a good practice because it’ll flag any issues with the database or file system, but if you’re confident in your process it’s fine not to do it
Doesn’t hurt, but not a big deal if you don’t. For the UUID make sure you keep the format consistent, in case that gets any future use that expects the UUID format.
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