I somehow accidentally left out the lib.flatten from mergeInputs. Without it, subtractLists won't ever remove anything from the inputs since the inputs will be a list of lists.
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@ -16,7 +16,7 @@
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let
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mergeInputs = name:
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(attrs.${name} or []) ++
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(lib.subtractLists inputsFrom (lib.catAttrs name inputsFrom));
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(lib.subtractLists inputsFrom (lib.flatten (lib.catAttrs name inputsFrom)));
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rest = builtins.removeAttrs attrs [
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"packages"
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