Update to use biom-format 1.2.0

This will fail Jenkins' tests because it has not yet been updated to install biom-format 1.2.0 via qiime-deploy. I'd prefer to let this fail and have the pull request reviewed, instead of updating qiime-deploy and having users end up with a broken QIIME 1.7.0-dev install until this is merged. I've tested this on my laptop (running the full test suite and the two IPython Notebook tutorials) and everything looks good.

Additionally, since I had to update the IPython Notebook tutorials, I removed the output of the fungal ITS tutorial. This matches how we are presenting the Illumina overview tutorial (i.e. we are only including the commands + explanations) and I think it makes sense to do it this way, because otherwise these notebooks get to be much larger than they need to be, and I don't think the output is really all that helpful (links are broken, etc.).

@gregcaporaso can you please review?