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Fix stalling in Pipeline command (#632)

* Fix stalling in Pipeline command

When a command (other than the first) in a pipeline wrote more than
64k to the stderr, and the output was consumed with the iter_lines
function, the whole pipeline stalled. Fixed by reading the output
of all commands where either stdout or stderr was set to PIPE.

* disable new tests on windows, increase timeout

* black & flake8

* trying to figure out what the extra items are

* test_pipelines: ignore empty lines

somehow stderr includes an empty line when run on pypy

* skip new tests on windows

* Apply suggestions from code review

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Co-authored-by: Henry Schreiner <HenrySchreinerIII@gmail.com>

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