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Since Slush took quite a hit due to the hacked Linode servers, I'm wondering how do mining pools protect their wallets from theft of file and theft of private keys in those files?

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If a pool makes a payout, the mechanism that performs the payout must have use of a private key. Therefore I don't believe there can be any secret to securing this private key beyond good operational security best practises. This would include operating with a minimum of "cash-on-premises", so the wallet used by the payout mechanism would only have enough BTC to cover payouts for the next few days, relying on refills performed by an entirely separate, manual process.

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    Multi-signature transactions will open a whole new world of ways to make Bitcoin-paying sites more secure. – Meni Rosenfeld May 11 '12 at 15:35

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