Fancy progress

This PR implements fancy progress tracking:

* Progress bar will automatically be shown if the ETA is more than a second.
* Progress will be displayed visually as a bar and also as a percentage number.
* The progress bar displays the ETA (estimated time of arrival). (Though, I'm using the simplest possible formula to calculate it right now.)
* The progress bar will display how long the simulation took after finishing.
* The width of the progress bar adjusts to the terminal width if Python >= 3.3 is used (otherwise it defaults to 80 characters)
* In an IPython notebook a fancy HTML/Javascript progress bar will be rendered.

This PR is an alternative suggestion to PR #476.
Oh that ... it's from the `clearoutputs.py` script. I configured it to run as a filter so that I never commit the cell outputs. But it seems to change the newline at EOF. Because of the filter I see that file always as changed and cannot switch branches as long as I don't commit that change or remove my filter. In this case I made a temporary commit and decided to figure out later what the best way to deal with this is.