User blog comment:D. Cello/Animus Hardware code decyphered/@comment-3130611-20110618164233/@comment-1153722-20110618165926

I think the "I AM ALIVE" referred to the fact that he is alive in some form inside the Animus. It is the reward you get after completing all the Rifts, and you get to meet Subject 16 afterwards simultaneously as you get the achievement. The "I am not alive" file might hint that he's not physically alive, and I think we'll get to see how he killed himself at Abstergo.