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On the Optimization tab of the preferences dialog you can set the file sorting criteria and order. Also you can exclude big files from the optimization process, which does make sense as sorting of big files does not improve system performace under most circumstances.
You can sort files by path, by size, by the creation time, by the last modification time or by the last access time either in ascending or descending order.
By default the program sorts files by path in ascending order and skips all files bigger than 20 MB.