Recent studies show that the color contains the leaves of the indigo plant and a clay mineral called palygorskite; but scientists were perplexed over the method of mixing the two to create the amazing color. They agreed it likely was heated with Copal incense, a tree resin, during the ritual, which somehow bound the ingredients to create the color.
The process of using the heat to absorb the indigo into the clay is the secret that appears to make the color so stable. Molecular x-rays show that the clay fibers contain channels filled with water molecules. When the clay is heated, the water is exchanged for the indigo, which is sealed in place by what scientists call a "gatekeeper molecule" which prohibits the indigo from escaping.
The indigo molecule becomes seared into the clay, creating an extremely stable chemical. In essence, the indigo-clay combination becomes a new compound.