Cracks in Toilet Bowl Serious

It's essentially an external kidney stone.

You can use various types of acid - sometimes a alternating approach of chlorine bleach (by itself) to kill the biofilm that's exposed and acid (by itself) to remove the "more or less limestone" is beneficial. The biofilm can prevent or slow the acid from getting to the underlying stony material, and it tends to have a layered structure.

Vinegar works, but slowly. Citric acid should work better (it's a stronger acid) but can be harder to find. Muriatic (aka hydrochloric) makes me a bit uncomfortable, personally, but there are commercial toilet cleaners that contain it. Be sure to use gloves and goggles if you opt for the stronger stuff.

If you are having trouble locating from what area of the tank is leaking you can add a blue colored food dye to the reservoir (tank) to see if it appears in the bowl. If you see the water is turning color then concentrate your search at the tank/bowl and/or flapper section. Although 4-5 years may not seem like a lengthy amount of time, for rubber and plastic parts it can seem forever. The flapper, if 4-5 years in service, should be replaced. Also make sure the fill valve, specifically the float, is not adjusted to high. It should cut out the water flow when filling about 1 inch below the overflow pipe that the flapper is attached to. The last place to look for the offending leak is the exterior of the bottom of the tank (this would be obvious as water would appear on the floor). The rubber washers that seal the tank to the bowl can deteriorate and crack as can the large washer that the flapper closes onto. The washer on the fill valve is on the exterior and one inside. Check with a flashlight for any water trails. One last place to check is the top of the fill valve were the float (if set up as such) is attached. If possible open the cap on the valve top and look for trapped debris that prevents the valve from closing fully.