housekeeping: update readme, add missing params to command builder, rename setup scripts

[uoefeb]

I'll go ahead and merge this, but as an FYI:

• prefix all setup scripts with "setup_"
• add .gitkeep to all data directories so the directories don't have to be created manually
• README:
  • update readme regarding directory structure (make documentation easier to maintain)
  • add presampled frame download links
• add validation_annotations_json parameter to command builder output since the training command now needs that too
• reorder sampling script to put transnet first