Refactors the upload to split on different filetypes

LRT uses ZIP files and the rest use CSVs, so I just have a small
refactor that splits up the processing and diverges depending on the
filetype.
Merge pull request #1995 from lukecampbell/qcprocess

Refactors the upload to split on different filetypes
Merge pull request #1996 from brianmckenna/m088_gradient

M088 - QC tables - adds gradient test CSV
Updates submodule for coverage model
add comments/documentation and refine debug
Merge pull request #1998 from MauriceManning/script3_rebase

CIDEVSTC-183 Integrate and Validate with Production System
Merge pull request #1997 from lukecampbell/cov

Updates submodule for coverage model
OOIION-1788: Enhanced preload supporting alternative agents per model
Cleanup preload exceptions
OOIION-1788: DataProduct supporting PDICT from agent mapped agents
Bumped ion-definitions
Bumped ion-definitions
Merge pull request #2000 from mmeisinger/fix1788_pre2

OOIION-1788: Enhanced preload supporting alternative agents per model
merge conflict resolution