How do I clean a root cellar under my porch to make it suitable for food storage?
Moisture is the ally of musty, moldy.

I would remove the stones, wash them in a household cleaner, such as Lysol. Wash down the walls and woodwork as well.  Setup a fan to dry out the area.  Run a dehumidifier in the rest of the basement during the summer.  Repeat using the fan if musty odors return.

Put down a vapor barrier on the ground, 6 mil poly minimum, pond liner is a very sturdy option.  Make the piece big enough to fold in the corners and contain the stones