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I tried to use sx, but it no longer works since bip62 (malleability fix). Nodes don't accept generated transactions, saying "high S signature".

What offline command-line tool would be the best?

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There are many command line tools for creating and signing raw transactions offline, most of them written in Python: pycoin, python-bitcoinlib, pybitcointools and others.

If you use Electrum wallet, it has command line tools for offline transaction creation and signing:

$ ./electrum help createrawtx
$ ./electrum help signtransaction
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