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STYLE: Fix acronyms, correct files names, correct doxygen class names, block...

Andrew Wilson requested to merge andrew.wilson/iMSTK:StyleFix into master

This further conforms style.

  • Replace acronym usage from all caps to first upper case. However, I left CD, IO, SOR, & VTK. In this MR mostly Pbd, Fem, & Sph were corrected.
  • Corrected file names to match class names
  • Corrected doxygen class names to match class names
  • Inserted many ///@{ & ///@} cases
  • Removed extra unneeded virtuals in many spots
  • Removed \briefs that just said "Constructor" or "Destructor"
  • Fixed a few class briefs.
  • Added some virtual destructors in base classes
  • Fixed namings in SWIG wrapper
  • Made a few classes have virtual destructors as they were inheritable
  • Fixed some typos/bad comments
  • Removed all namespace endings, then turned on commented namespace endings in uncrustify so it would do it. These were being used in about 60-70% of classes. Varying from "imstk", "end namespace imstk", "namespace imstk". Now uncrustify places them.

Resolves: #399 (closed) & #398 (closed)

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