curate functions on pkgdown site to improve documentation

[k-doering-NOAA]

Use the user manual classifications: https://nmfs-fish-tools.github.io/SSMSE/manual/intro.html#funs

Some exported functions are not useful to users (they are exported so examples can run, I believe).

How to curate pkgdown reference: https://pkgdown.r-lib.org/articles/pkgdown.html#reference