overview tutorial updates

fixed merge conflict from @wasade's #1334, plus various other updates (including fix to get this to work out-of-the-box with ``pip install qiime`` - see #1696).

[Here](http://nbviewer.ipython.org/github/gregcaporaso/qiime/blob/tutorial-updates/examples/ipynb/illumina_overview_tutorial.ipynb) is the rendered notebook, if it's useful for review.
Can you make these rendered as bold instead of italics? It's a little hard to read the way it is now.