Fix unable to parse error(As reported by SJoseph)

Ignore EOFError raised by stderrout.read_nonblock, since with
sufficiently big stdout, small stderrout and small buffer_size, err
will reach EOF before the stdout is completely read. This would
cause the graders output to be truncated.
Remove unnecessary comments.
travis
More exhaustive tests for run with timeout
Fix unable_to_parse bug as reported by SJoseph.

This bug has another aspect that becomes apparent when we read
the output of the spawned process so slow, that the process
terminates long before we read its whole output. This alone is
not bad, however the condition thread.alive? was used in the while
loop. This led to the premature termination of run_with_timeout.
Merge branch 'unable_to_parse_fix' into per_exercise_due_date_and_grace_period