Just encountered this when trying something related to another thread. I have two pictures attached, simply showing the box that I checked/unchecked while testing. Whether the box is ticked or not, clicking the 'swap' button or using the shortcut (CTRL-TAB) does not produce a confirmation box. The "ConfirmSwapSides" line in the GlobalSettings.xml file is set to TRUE.
I have also re-opened FFS between changes and no change in behavior has been observed.
Bug: Warning "Please confirm you want to swap sides" not displaying regardless of selected setting
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The warning is only triggered after a comparison has filled the file list.
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The difference in the order of operations is negligible, so I think a warning for one justifies a warning for the other. I think accidentally swapping sides before comparing is more likely to go unnoticed than the other way around, seeming to justify the opposite warning behavior.