Update QIIME biom-format docs

Fixed some typos and updated to use ```biom convert``` command.
Update 18S tutorial to use ```biom convert```
Update shotgun tutorial to use ```biom convert```
Update contaminant filtering tutorial
Update cytoscape tutorial
Update sourcetracker tutorial
Update otu_category_significance.py
Update contaminant tutorial with summarize-table
Update overview tutorial (summarize-table)
Update biom table tutorial (summarize-table)
Update procrustes tutorial (summarize-table)
Update sourcetracker tutorial (summarize-table)
Update illumina proc tutorial (summarize-table)
Update core_div_analyses (summarize-table)
Update fungal ipynb (summarize-table)
Fix ipynb error
Update illumina overview tutorial ipynb
Update illumina overview tutorial cells

to be clearer
update overview tutorial shell scripts
Update core_div_analyses with summarize-table