I tried with cat -A and other editors to confirm multiple times that the issue is with geany editor only.

You confirmed what with cat -A, show all your workings, I can't see over your shoulder.

I cannot replicate any bug in Geany, if I open a file with a newline at the end the extra empty line is shown, if I open a file with no newline at the end no extra line is shown. This is what is the intended behaviour, and as far as I can see Geany is behaving as intended.

You need to provide an exact set of steps that demonstrate your issue, if it can't be replicated it can't be fixed.

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