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This appears to be a problem with sqlite3 itself.
$ cygcheck -c sqlite3 Cygwin Package Information Package Version Status sqlite3 3.6.21-2 OK $ ls $ echo -e '.schema\n.quit\n' | sqlite3 tst.db $ /bin/ls -1 | cat -A M-cM-)M-^CM-gM-^QM-^\M-fM-5M-%M-eM-1M-0M-gM-^EM-3M-fM-%M-,M-fM-^UM-4M-eM-0M-3t$
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