DOC: updated for the moving pictures tutorial 1.9.0 data

~~**NOT READY FOR MERGE**~~

Various updates, including:
 * collapsing all inputs into a single fastq file (which is a more common use case than multiple fastq files)
 * use of the ``--recover_from_failure`` option for ``core_diversity_analyses.py`` to add categorical analyses (a big time saver that users should be aware of)
 * addition of time axis to Emperor plots
 * improved naming of some of the metadata in the mapping file
 * addition of some recent references
 * some text and code clean-ups

~~Working on some strange clustering of samples - it's possible that I have some mislabeling here.~~
This section seems out of order. Can you move the two emperor commands above this line, and swap the order of the two sentences on this line? Also, remove *When you generate these new plots,* from the swapped sentence.