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To answer Phyz's original question with complete clarity:
"I don't wanna remember nothing... Nothing! And I wanna be someone important... like an actor." Cypher, while being disgruntled but not insane, certainly believed that the matrix could reinsert both his body and his mind, changing his entire belief structure, personal memories, personality, everything that he thinks he is, into the system.
So, if Cypher can be a zion rebel, jack into the matrix and become a whole new person, then he can also be taken back out of the matrix *after* being changed (into an actor, supposedly named Reagan, with a real history of being (lu)cypher... wink wink). So the technology for a total neuronal take over is within the matrix, Smith just happened to gain that power in a very hacked, on-the-fly sort of fashion.
Thus, Bane jacks in, is taken over (and the change is both in his matrix avatar AND his personal, physical gray matter), and jacks out... as Agent Smith.
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