Refactor Action/Condition managers and collections, and PulseConfiguration AND Patient Configuration ctors not accept a Substance Manager
- Pushed that requirement to methods that need it and to be provided by the caller
Should simplify construction and usability of these various classes (especially conditions)
Also changed Data request creation to take substance names, and not substances (no need to load things off disk to fill out a name)

Update Hydrocephalus study outputs and added in all overrides
Simplified our full preliminary data combination set
Added in a python analysis file to be filled out