stdio text streams are using Unix format.
Under Cygwin, text files are Unix formatted: lines are terminated by linefeed characters, which match the newline line terminator character in C, so that C streams don't have to perform any line ending conversion between the internal and external representation
The Windows native text file format uses carriage return plus line feed to terminate lines. When Cygnal creates a text mode stdio stream, it should open it in Windows text mode. Cygwin has the internal support for this (it even supports the Microsoft "t" mode flag in fopen); it's a matter of some minor changes in the code.
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