Fix pkgdown configuration for reference

[maelle]

Some topics are missing from the configuration file.

 Error in check_missing_topics(rows, pkg) : 
  All topics must be included in reference index
• Missing topics: CoordinateCleaner-package, buffland, buffsea, countryref, institutions, pbdb_example, plot.spatialvalid, write_pyrate

Note that for topics you do not want to include in the index you can create an "internal" section https://pkgdown.r-lib.org/reference/build_reference.html?q=internal#missing-topics

You can also use the @keywords internal tag and redocument for, say, the package manual page.

To check all topics are listed, after editing the configuration file you can run pkgdown::check_pkgdown().

[maelle]

@azizka