Miscellaneous bugfixes and cleanup

[brbass]

Summary

• Removes the old, non-functional volume calculation from SPH and requests Voronoi cells from RK instead.
• Adds missing includes across several files.
• Moves NodeIteratorBase stream operators from the inline header to the source file.
• Fixes the Johnson-Cook damage model to avoid circular dependencies
• Adds parallel GenerateRatioSphere in 2D.
• Includes material internal energy in the generic node distribution.

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ToDo :

• Annotate RELEASE_NOTES.md with notable changes.
• Create LLNLSpheral PR pointing at this branch. (PR#)
• LLNLSpheral PR has passed all tests.