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I'm trying the latest version and it's still pretty much unusable on large files (and by "large files" I mean like 10MB).
It can make N++ hang maybe for hours and it's not even possible to cancel the compare process. I don't know if it's the size alone or the number of lines that causes this.
If it's not possible to fix this, maybe you can add a warning when a user tries to compare large files.
btTeddy and harveyadcock