“They took away the old timbers from time to time, and put new and sound ones in their places, so that the vessel became a standing illustration for the philosophers in the mooted question of growth, some declaring that it remained the same, others that it was not the same vessel.”
Plutarch, translated by Bernadotte Perrin, Life of Theseus · Theseus 23.1 · read it
Kept because the oldest puzzle about identity is a maintenance log. Every long-lived codebase is this ship. The question of whether it is the same system matters less than who still knows why each timber was replaced.