DOC: updated for the moving pictures tutorial 1.9.0 data

~~**NOT READY FOR MERGE**~~

Various updates, included collapsing all inputs into a single fastq file (which is a more common use case than multiple fastq files) and use of the ``--recover_from_failure`` option for ``core_diversity_analyses.py`` to add categorical analyses. 

Working on some strange clustering of samples - it's possible that I have some mislabeling here. 
Can we drop the `illumina` directory entirely from the tutorial? All commands read and write data within `moving_pictures_tutorial-1.9.0/illumina/` (except for the parameters file). This makes the commands longer than necessary since the tutorial doesn't use the 454 data and the Procrustes tutorial has its own version of this data.