I noticed that there is no new line at the end of the file if the option Ensure new line at file end is disabled and the file is closed. I checked that with a different editor (not with Geany). Only on re-opening the file in Geany the new line appears in the editor window - but it's not in the file. Not sure if that helps.

I also had this issue wherein the geany editor shows there is a newline at the end of file but when I open the same file on vim editor, there is no newline. This leads to ambiguity and hence should be considered a geany editor bug in my opinion.

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