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Just as an info:
I am no longer supporting the old Compare plugin.
The newest plugin is called ComparePlus (its current version is 1.2) - it is supported.
Unfortunately both plugins are not taking into account the line endings of the files - those are always ignored as the compare process works on line-by-line basis (regardless of the Ignore settings). I am not planning to change that because line endings are not visible in Notepad++ (unless you have explicitly configured that but then you will directly see line endings differ) and then one will see that there are changes between some lines but that changes are not apparent (they are only in the invisible line endings).
I can probably implement a warning about comparing files with different line endings but that will be generic and not line-by-line (for example a case when you have one line only with LF and some other lines in the same file with both CRLF will not be detected).
I added a warning message on each new compare if the line endings of the compared files are not the same and informing the user that the compare process will ignore that fact. This change will be available in the next ComparePlus plugin release. Your screenshot is about the older Compare plugin which is no longer supported (by me).
Two identical files, one w/c has CRLF and another w/c has LF as line ending can be detected as matching despite having whitespaces not ignored.
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