\documentclass{article}
\begin{document}
First paragraph ending with \verb|^^J|,
with text from the second line ending with \verb|^^M^^J|,
as well as the third one ending with \verb|^^M^^M^^J|.
Thus the fourth line must be in its own paragraph,
and \verb|^^M| after the comma is converted to a space.
\input{newlines-input}
Hence the final line must be a separate paragraph.
\end{document}