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Fixing navigation setup for PHYS/LITE trains

Zach Marshall requested to merge zmarshal/athena:21.2_PHYSandLITE_Tests into 21.2

When running both PHYS and PHYSLITE (or in fact PHYS and any other derivation), there was an issue in the navigation tool setup. This change further isolates the setup in PHYS from that in other derivations.

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