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Both beyond compare 3 & 4 use binary compare when compare folder. Many files are actully have same content but show as diff(red color), I know it due to line ends difference between linux and windows, but I don't find a way to change that in options.

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The default Folder Compare settings compare file size and modified timestamp.

To compare the text contents of files in the Folder Compare and ignore line ending differences (Windows CRLF vs Unix/Linux LF), click the Rules toolbar button (referee icon). In the Comparison tab, check Compare Contents. Select Rules-based comparison.

To make Rules-based comparison the default setting for new Folder Compare sessions, change the dropdown in the dialog from Use for this view only to Also update session defaults before you click OK.

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