Renames output folders so outputs are better organized by section of pipeline that produces them

[taylorreiter]

futzes with folder names so output folder structure is easier to navigate.

I may add numeric prefixes (00_read_qc, 01_assembly, 02_orthofuser, 03_decontamination, 04_evaluation, 05_annotation), but not sure it's necessary right now.

~#5, #9, and #11 should be reviewed before this one.~ done