Allow for settings to be partially updated

[ChrisSchinnerl]

Right now when we update a setting, we need to update the whole thing. The problem with that becomes clear when updating things like the autopilot config where the autopilot might want to only update the period but has to specify every field of the config. This causes a race if something else is trying to update a different field of the settings.

To fix that we should change the fields of the settings we set to pointers to make it clear which settings were set by the caller and then only update the ones that were set.