use celltagpreprocessor to remove parts of cells and updating running code module

[choldgraf]

This PR does a few things:

• Removes the use of a custom template for removing inputs/outputs/etc because we discovered the nbconvert "TagRemovePreprocessor"
• Fixes up the "run a notebook" code to use the ExecutePreprocessor
• Uses the RegExpRemovePreprocessor for removing empty cells
• As a result, we no longer need nbclean so we're removing that dependency (which is actually pretty heavy)
• One side effect is that stderr will now show up in the output, though we can take that out later pretty easily

[choldgraf]

Merging this because I don't think it changes the behavior of the tool at all, it's all under-the-hood simplification