The default newline output by E-on-Java's file IO is now the canonical linefeed ("\n") rather than the platform's native newline.
This is controlled by the static variable org.erights.e.develop.format.StringHelper#TheLineSeparator, so if we change our minds, we should be able to fix it in this one place.
The reason for this fix is that there are really only two conventions left in the world: "\r\n" on Windows, and "\n" on everything else. It seems that virtually all Windows software other than Notepad is compatible with either, so it just isn't worth the complexity of living with two conventions. This is much like the reason that E always uses "/" for a directory separator, hiding whatever the platform might use instead (e.g., "\\").
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This has been implemented as stated above. However, we still seem to observe "\r\n"s in some output files, such as trace files I think. Until this is tracked down and fixed, this bug report is still open, but it's of low priority.