I don't know about limestone, but I had a rock wall built that used granite boulders in some places to add stability and they get dark and "dirty" looking. I've had them pressure washed (gentle pressure) and they look so much better when clean to me. I love moss covered elements in the garden, but I loved the look of the rock wall when it was first built, so for now, I like it when it's restored closer to that newness. Your wall looks like it could be used for sitting? If so, clean might be more appealing. Try cleaning it one time and see what you think. If you don't care for the look, it will soon be "dirty" again and you can let it be. Or you could encourage moss to grow and maybe it would replace whatever organisms are just dark and dirty looking.

The vinegar isn't strong enough to clean 'oil' prints like skin oils (foot prints). You need a better 'degreaser'. Your situation is one of the most complained about. Dark, low-gloss flooring showing oil prints. You can try a spritz of Windex on a tile, let it sit for 30 seconds then wipe it up. Spritz the tile again and then wipe up immediately with a NEW cloth. Walk away for a n hour or so. Then go back and 'reassess' the tile you just cleaned. If you can see the difference then you know you are on the right track. One of the issues with 'air drying' is the water evaporates off but the GUNK is left behind. It's kinda like smearing mud around without removing the mud. A towel dry is a better option for low-gloss floors. It ensures you get the water AND the gunk off (the stuff you were trying to clean in the first place).

This is what I found on the product. If you want to read the actual manufacturers care and maintenance, you need the Acrobat Reader. https://get2.adobe.com/reader/ However, they also recommend bona products to clean the floor. ENCLAVE COLLECTION The 11 references are softly distressed with a range of colors and treatments of the wood surface. ½ ‘ in thickness with a 2mm sliced oak veneer these 75” long by 7” wide planks are offered at a competitive price point. The matte finish mimics the “velvety” appearance of an oil floor but it can be maintained just like any other acrylic urethane coated wood floor. The profile is T&G and can be glued, nailed and floated but only installed on or above grade. SPECIFICATION: Plank Dimensions7.48” x 74.80” x 1/2″Sq. Ft./Carton31.09ConstructionEngineeredSpeciesOakFinishAcrylic Urethane with Aluminum OxideInstallation MethodTongue & Groove, Glued, NailedInstallation LevelOn or Above Grade LevelResidential Warranty25 YearCommercial Warranty 3 Year Light Commercial Complies with the Lacey Act Complies with CARB Phase 2 formaldehyde emissions standard CCR 93120.2(a)

That HM recommendation gave our tile layer mild heartburn. I think it‘s just such a rare spacing in the US and she warned against the high-maintenance cleaning regime that such a grout gap would demand. She demonstrated a few options up to .5” and after discussing it we compromised at .375” or 9.53 mm. She is a highly skilled and sought after tile layer so I trusted her opinion. The compromise still achieved the look I wanted so was happy with it.