While yeast is proofing, in separate bowl, using wire whisk, mix flours, salt, and thyme. Once yeast is foamy, add flour mixture and mix in stand mixer fitted with dough hook, or knead by hand until dough is smooth and elastic (about 7 minutes). Stop mixer halfway through, remove bowl, add pine nuts, and then knead a few times by hand to incorporate before returning to knead with the dough hook. Place dough in oiled bowl and cover with lid; refrigerate for 6 to 8 hours or overnight.