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Is there a way to configure cgminer to accept valid but nonstandard transactions for mining?

If not, where, theoretically, would be a good place to look if I was interested in mining nonstandard transactions into the blockchain, i.e. what must I modify in what node/client code?

Alternatively, would it be enough to modify a client to relay such transactions to cgminer without modifying the mining package itself? Does cgminer also verify that a transaction is standard?

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I suggest you go and read about just what cgminer is presented with, in most cases it is just the header which has absolutely no bearing on the content of the block. It does not, and can not in most situations know what the work it has been provided with actually is.

The node providing work must be modified slightly by changing the isStandard checks, which you can find in main.cpp of the Bitcoin core client. There's not really that much interesting you can do at present without making your block invalid, but it's easier just to submit them directly to eligius.st which is a pool that already accepts certain nonstandard transactions. The chance of a user solo mining a block is vanishingly tiny at this point.

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