Nightly testing needs further fixing / upgrades

[CodeByDrescher]

CLI has a number of bugs we need to fix to get things to an acceptable state

1. Python reliance removed, and plotting / logging done java side [COMPLETE]
2. Nightly testing scripts need updating, and new mode added to collect testing results [COMPLETE]
3. Missing features and bugs in CLI need solutions [IN PROGRESS]
4. Need to convert nightly testing to VCML-starting archives, not pre-exported archives (this produces better testing) [QUEUED]