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If you bound Command+Enter to the command eval-sel-in-shell then it'll always do that command because it is active all the time regardless of whether the Python Shell tool or editor has keyboard focus. I don't think there's a good way for the IDE to know whether you want it to do evaluate the current selection in the Python Shell or submit AI Coder's message to the AI provider.

What might work is to instead bind Command+Enter to the command shell-ctrl-return, which is used internally to make Ctrl+Enter work. However, that's not going to do the same thing as eval-sel-in-shell in context of the Python Shell tool.