The transcript extraction used len(history) to find new messages, but
history includes session_meta entries that are stripped before passing
to the agent. This mismatch caused 1 message to be lost from the
transcript on every turn after the first, because the slice offset
was too high. Use the filtered history length (history_offset) returned
by _run_agent instead.
Also changed the else branch from returning all agent_messages to
returning an empty list, so compressed/shorter agent output does not
duplicate the entire history into the transcript.
