Doxygen updates#44
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…ter adapted from MAGMA and SLATE.
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Updates doxygen template and config for doxygen 1.12.
Adds missing doxygen groups. (A few are fixed in the SVD branch.)
Fixes missing and mis-named parameters, and other fixes.
Adds filter used in MAGMA and SLATE to recognize Latex-style
\[ ... \]and$...$commands.Updates README.