There isn't a manual deprecation step, because the agent has no context outside what the human gives it. Deprecation happens when conflicting information is given ("you want to do this but this note says you tried it before and it failed, what do you want to do?").
At that point, either the human decides to go for it and the new decision is noted, and the old decision is superseded/removed, or the human says "wow I'm sure glad I'm using gnosis" and everything is left as-is.