Review run_command function and clean up #102
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As per the previous PR, update run_command to use Popen.communicate() in case of large output from the command. The stdout.readlines() would prevent blocking, however communicate ensures all handles are cleaned up once the process has completed. Also tidy up the code inside run_command.
run_command accepts a sort argument which causes the line output from the command to be sorted. Can only do this with a list hence we're moving back to stdout.readlines() which creates a list of lines. Also clean up the subprocess.Popen call.
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