Remove using declaration for namespace `chrono::geometry` from headers.

Fix issues related to this change.
Remove even more using declarations from headers:

- `collision` from ChAssembly.h, ChMatterSPH.h, ChNodeBase.h, ChParticlesClones.h, and ChIndexedParticles.h
- `pneumatics` from ChLinkPneumaticActuator.h

Fix issues related to these changes.
Cleanup ChMitsubaRender:

- remove using declarations from header file.
- use const references where appropriate.
Remove `using namespace chrono::geometry` from various header files.