How do you get the possible routes to use?

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Min. Cost Flow, where the cost function is a combination of uncertainty and fees. This is the implementation of Pickhardt-Richter's idea. https://arxiv.org/abs/2107.05322

I mean are you calling any of the other CLN commands/plugins when you are carrying out the min cost flow process?

No, MCF is done with a model of the network. RPC communication with CLN is needed to send the onions, we call sendpay.