remove ceramic floor tile replace with new tile

We had a ceramic tile floor installed in our new home which developed serious flaws in the finish. The tiles were replaced under warranty. Cracks started to appear a few months latter. The cracks are in the tile not the grout, they run north-south and east-west, and in high traffic and low traffic areas and now the floor creaks when walked on. The contractor beat the bejesus out of the floor with 10lb sledge and electric jack hammer removed the tile and cement. When finised the floor was rough, he put down a layer of cement and placed the tile in it. Latter I found out he was supposed to put down new plywood or prepare the floor with screed?? Note: the adjacent bathroom has the original tile, blemished but not cracked! The floor is supported on 2x10 spruce, single span <12', 16"ctr, blocked then strapped with 2x3's. The first layer of plywood is 5/8's weatherproof, glued and screwed to the joists. the subfloor is 5/8wp plywood screwed every 4" with the sheets crossways to the 1st layer. After this tile job is removed how is the floor supposed to be prepared for new ceramic tile. Can someone help?

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