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Ensure stdout/stderr are flushed

Calls to out.stdout_bytes() are rarely not being flushed to stdout. This
has manifested as sporadict failures in t2400-diff.sh, especially with
Python 3.4 and 3.5.

The issue is repaired by explicitly flushing in out.stdout_bytes() and
out.err_bytes().

Also remove the misleading Output.write_bytes() method which is unreachable
since Output.__init__() always dynamically reassigns the method.

Signed-off-by: Peter Grayson <pete@jpgrayson.net>

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