In this situation the best thing to do might be to make a choice, go with it for a while, and see how well the subsequent changes cluster. If all the changes in patches implementing features tend to be in the same place, you got it right. If not, time to reshuffle.

Making a code layout like this is effectively making a prediction about what future changes are likely to entail. Predictions can be wrong, so we want to be able to change anyway.