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I think that Twain is reflecting on Tom's apprehension and lack of experience in stealth robbery,
His courage and confidence were high, up to this point, but both began to waver a little now. Suppose he should make a noise, by some accident, and get caught—say, in the act of opening the safe? Perhaps it would be well to go armed. He took the Indian knife from its hiding place, and felt a pleasant return of his wandering courage.