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With Geany 1.28 Release for all three file types as attached above the status bar shows the mode correctly (mode:CR / mode:CRLF / mode:LF).
Current Git 2a2ae72 on Linux gets all three right, so its something strange about Windows or nightly builds.
The code for determining the line ending is here and as you can see its not related to Windows or Linux. I notice it has a bug where it will undercount CRs for successive blank lines in CR only files, but thats not this. I am not aware of any change here lately, but your nightly is a couple of months old, you might try the latest.
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