All seven commandments are erased. What is the new commandment and how has it been true from the beginning?

At the end of the book, in Chapter 10, there is only one commandment left.  It is

ALL ANIMALS ARE EQUAL
BUT SOME ANIMALS ARE MORE EQUAL THAN OTHERS

This has always been true because the pigs and, to some extent, the dogs, have always been "more equal" than the other animals.

Throughout the story, the pigs have enjoyed more privileges than anyone else.  All the leaders have been pigs.  The pigs, for example, have been the ones who got to have all the milk whereas it used to be given to the hens.  In addition, the pigs get all the apples.

Things like that show that the pigs have always gotten more than their fair share.