fix misuse of fcntl

We were using F_SETFD/F_GETFD to set O_NONBLOCK, but this is meant to be used on
the status flags, not the file descriptor. We correct this to use
F_SETFL/F_GETFL. Surprisingly this bug caused no visible misbehaviour on Ubuntu
Linux, macOS or FreeBSD. It was detected by a user on Arch Linux under WSL.

Github: related to #140 "Unit test fail on smt-simplify.m"