What can you do with planets that have a Stone Age Primitives modifier?

Stone Age primitives are actually a third state in-between the pre-sentient races that you can uplift and the fully sentient primitive civilizations that you can observe.

This is explained on the Stellaris Wiki's Pre-FTL Species Page:

There is a third possibility of non-FTL races, which are the stone age primitives. They appear as modifier on planets. If the policy for native interference is not Unrestricted, then the empire will be unable to colonise the planets. Therefore a pacifist or xenophile empire (or the fanatic versions) can't chose "unrestricted", and will be unable to colonise these planets.

So you might not be able to interact at all. Perhaps they will advance to the Bronze Age at some point and you can observe them. It's not clear if that's a possibility.

If you can colonize, though, here's what you can do once you get there:

Known Variations:

• Voluntarily retreat to Enclaves rather than contest the primitives for the land: Places a number of primitives on the surface map as tile blockers. Apparently these blockers cannot be removed, though they provide Social Science adjacency bonuses.
• Antagonize the aliens: fewer tile blockers
• Enslavement: No tile blockers. The new species appears as enslaved pops on the planet. The slaves can be emancipated, and integrated into the empire. Useful if a pop is neeeded to colonize worlds of the same type as their homeworld. Option is only available if slavery is enabled as a policy.

I think I actually had this happen on a planet in my current game, but I was confused because there was also a Pre-Sentient race on the planet. I uplifted that race, and was surprised to find that the Stone Age primitives continued to live in the reservations.

There's no way to do anything with planets that have the Stone Age Primitives as a xenophile or a pacifist without modding the game, doing so, however, is extremely easy. Open the file \common\game_rules\00_rules.txt and change the following text

#Root = country
#This = planet
can_colonize_planet = {
    if = {
        limit = { 
            AND = {
                has_modifier = "stone_age_civilization"
                ROOT = {
                    NOT = {
                        has_policy_flag = interference_full
                    }
                }
            }
        }
        custom_tooltip = {
            text = "NONINTERFERENCE_DIRECTIVE"
            always = no
        }
        else = {
            always = yes
        }
    }
}

to this

#Root = country
#This = planet
can_colonize_planet = {
    always = yes
    }
}

Then restart the game and you'll be able to colonize the planet as though you had the Unrestricted Native Interference policy.