get reactive transport working in ATS master

[ecoon]

Clarify initialization of Chemistry and ATS

@ecoon

• move chem_engine_->InitState() into setup?
• move initial conditions state list into chemistry pk and out of state initial conditions list
• make sure chemistry PK Initialize calls secondaryvariable update for saturation, anything else it needs in the dag
• make sure flow + reactive transport inits flow before reactive transport

Fix Seg Faults in Alquimia + Amanzi

@ajkhattak

• seg fault in AmanziChemistry::Alquimia_PK::CopyAlquimiaStateToAmanzi() (some missing setup of

Add Chemistry Regression Tests

@ahmad and @dasvyat

• stream_decay_ingrowth.xml

[ecoon]

Capability is working as of #64

Tests still need work, but those should be tickets in other repos.