I can copy a file fine using the copy command in the Exec node, but is there a way the filenames could be based on a payload variable?
Yes.
Also, you might want to look at node-red-contrib-fs-ops
If you still want to use the exec node then it can be passed the complete command (so you can build that up before passing it to the exec node) by leaving the Command field empty and selecting Append Payload. Alternatively, where appropriate, you can put the bulk of the command in the node and then just pass parameters in the payload, again with Append selected.
Can you show me an example of that?
With fs-ops
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