Removing set/getMisc(), docs, etc.

[gregorgorjanc]

This is to close #584

All checkc pass on my end so I think this can be merged in, but @janaobsteter have a look please.

[gregorgorjanc]

I get this errors in the GitHub action

...
── Sitrep ──────────────────────────────────────────────────────────────────────
✖ Bootstrap 3 is deprecated; please switch to Bootstrap 5.
ℹ Learn more at
  <https://www.tidyverse.org/blog/2021/12/pkgdown-2-0-0/#bootstrap-5>.
✖ URLs not ok.
  In DESCRIPTION, URL is missing package url (http://www.simplybee.info/).
  See details in `vignette(pkgdown::metadata)`.
✔ Favicons ok.
✔ Open graph metadata ok.
✔ Articles metadata ok.
✖ Reference metadata not ok.
  In _pkgdown.yml, 3 topics missing from index: "getMisc", "mapLoci", and
  "setMisc".
  Either use `@keywords internal` to drop from index, or
...

but I don't see getMisc() anywhere in my codebase

grepall . getMisc
./.Rhistory
./NEWS.md
./docs/articles/A_Introduction_to_honeybee_biology.html
./docs/reference/addCastePop.html
./docs/reference/buildUp.html
./.git/logs/HEAD
./.git/logs/refs/heads/devel
./.git/COMMIT_EDITMSG
./.Rproj.user/2472D3BB/sources/session-5f57f60a/5D06C4D6-contents
./.Rproj.user/2472D3BB/sources/session-5f57f60a/7650117D-contents

grepall . setMisc
./NEWS.md
./.Rproj.user/2472D3BB/sources/session-5f57f60a/5D06C4D6-contents
./.Rproj.user/2472D3BB/sources/session-5f57f60a/7650117D-contents

Any clue what we have to do @janaobsteter ?

[janaobsteter]

@gregorgorjanc , this is coming from pkgdown. I know there is a list of functions that it needs so I'm guessing those docs didn't get udpated. @LStrachan was handling this, not sure if we've ever documented how to update this.

[gregorgorjanc]

I have now found these autogenerated files, but indeed don't have a clue how to use the pkgdown to generate them :( Aha, we have the process described in #497, but I now have to move to another task - enough of SIMplyBee for today I am afraid. Maybe we merge this PR in @janaobsteter and deal with the pkgdown issue later in #595?

[janaobsteter]

@gregorgorjanc , I've just left three tiny comments and then we can merge