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