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When I run the joinmarket `wallet-tool.py` script it shows me six "new" address at mixdepth 0. Do I then send BTC from my bitcoin-core wallet to those? Or can/should I just send BTC directly to one of those addresses when I do the initial purchase.
The addresses listed by wallet-tool.py are in your joinmarket wallet. bitcoin-cli might give you the same information, but I would use only wallet-tool.py. Obtain some bitcoins and send them directly to the first unused address listed in mixdepth 0.