Maybe because clisp upstream decided to read from pipes with crlf line-endings, so \n will not end a line. Only the cygwin release reads from pipes binary. Which makes more sense to cygwin, since we (cygwin) cannot deal with crlf and we want to pipe streams with line endings to clisp.
Otherwise I see no difference but i haven't tested the new named pipes yet.
2012-02-07 17:34:45 PST in CLISP - an ANSI C...
