Feature/55832896 sync manager 3

What this does
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 - This reworks the model sync methods to handle deleted objects. 
 - This moves TestRunCase from Additions to Models (How it was there in the first place...)
 - This updated most models to use dictionaries vs arrays for everything.
 - Handled sync properly :)

What this doesn't do
---
 - Handle the "active" model.

cc @joshpc @j-mutter @bgulanowski 

Please review!