Sometimes I'll compare by copy/pasting into the window instead of opening a file from disk. When opening a file from disk, the line end style is detected and used in composing the merged result. This detection does not happen when pasting instead, leaving whatever line end style is already there, which can result in Bad Things. (Leaving the line end style when pasting part of the content is understandable, but replacing the whole content of the window or pasting into an empty one should do the detection.)
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