The micro transaction fee only applies to the the 'out' side.
Right, but every TxIn has to have a corresponding TxOut (except for GENERATE/coinbase transactions, but those have their own rules). So if you want a 0 BTC TxIn, you've gotta first pay yourself with a 0BTC TxOut and that'll trigger the fee. TxIns don't contain a value, the value is in the corresponding TxOut...
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Anyone who is accepting 'bad' transactions and returning good coins deserves to give their money away.
But you agree that it wouldn't be OK for a 'refundtransaction' API call to make it easy to do that, right?