Overwrite run_cell to stream outputs to stdout/stderr when --log-output is set
Overwrite run_cell to stream outputs to stdout/stderr when --log-output is set

The main differences between this and the run_cell from 
ExecutePreprocessor is the addition of the streaming outputs and moving 
the wait for execute reply to after the iopub. This breaks the 
assumption that all of the iopub messages have been received by the time 
that they are processed.

nteract/papermill,nteract/papermill