Doc fixes

A lot of documentation fixes:

 * mainly to remove `\tabular` macros in `@return` sections and or redundant `\itemize{}` or `\describe{}` environments.
 * add links to functions in **neotoma** where these were just marked up as `\code{fun_name}`
 * edited the function names from the old plurals to the new singular names
 * removed trailing whitespace
 * add some Rd macro where markdown backticks had been used

Essentially this is to try to get the manual PDF to build. This is the first tranche of changes. More coming in the next set of commits.