hdf5doc

_ PDF sync-up (made sure the portions of the UG that are 
used to generate the PDF match the portions in the rest of 
the doc)
_ Made HTML formatting changes to match the format in the 
other chapters (quoting attributes, function names, 
quotation marks)
_ Updated the captions, headings, capitalizations, section 
numbering
_ checked use of deprecated functions
_ deleted unused footnotes