Mid year cleanup

This issue tracks tasks for a mid-year package cleanup.

## Supercharge your pkgdown website

- [x] Verify that website URL is listed in `_pkgdown.yml`
- [x] Verify pkgdown site is using epiversetheme
- [x] Check for manual specification of Bootstrap version (currently 5)
- [x] Add logo to `epiverse-trace/hex-stickers`
- [x] Use svg version of logo
- [x] Verify logo is properly detected by pkgdown & r-universe (path and name need to be exactly `man/figures/logo.png` or `man/figures/logo.svg`)
- [x] Add a pkgdown reference index: https://pkgdown.r-lib.org/reference/build_reference.html#reference-index.
Use selectors (e.g., `starts_with()` or `contains()`) to select functions rather than an explicit list. This serves the double purpose of checking that functions follow a coherent naming scheme.
- [x] Verify intro vignette appears under 'Get started'
- [x] Verify vignettes are ordered correctly (if applicable)
~- [ ] Verify all images include helpful alt-text~

## Developer tools

- [x] Update lintr, roxygen, usethis, testthat, devtools to the latest version on your local computer: `pak::pak(c("lintr", "devtools"), dependencies = TRUE)`
- Copy from packagetemplate:
~- [`.lintr`](https://github.com/epiverse-trace/packagetemplate/blob/main/.lintr) config file~ see #184
- [x] [GitHub Actions worfklows](https://github.com/epiverse-trace/packagetemplate/tree/main/.github/workflows)
- [x] [`tools/`](https://github.com/epiverse-trace/packagetemplate/tree/main/tools) folder
- [x] [`tests/spelling.R`](https://github.com/epiverse-trace/packagetemplate/blob/main/tests/spelling.R)
- [x] [`tests/testthat/helper-state.R`](https://github.com/epiverse-trace/packagetemplate/blob/main/tests/testthat/helper-state.R)
- [x] [`tests/testthat/setup-options.R`](https://github.com/epiverse-trace/packagetemplate/blob/main/tests/testthat/setup-options.R)
- [x] Run `spelling::spell_check_package()`

## Misc good practice

- [x] Change files ending in `.r` to `.R` in `R/` and/or `tests/testthat/`"
- [x] Review usage of `# nolint` comments. New versions of lintr may have squashed previous bugs
- [x] Update year in license file

## Documentation

- [x] Use roxygen2 markdown syntax (`usethis::use_roxygen_md()`)
- [x] Add a related project section at the end of the `README`
- [x] Check that all URLs are working, up-to-date, and leading directly to the expected page: `urlchecker::url_check()`
- [x] Add package-level documentation page: `usethis::use_package_doc()`
- [x] Move package-level imports to the package-level documentation
- [x] Verify that all `@import` and `@importFrom` import functions that are actually used in the relevant function
- [x] Identify potential for [reuse in documentation](https://roxygen2.r-lib.org/articles/reuse.html)
- [x] Run `devtools::document()`

## `DESCRIPTION`

- [x] Verify if any package in `Remotes` is still necessary
- [x] Check that [package `Description`](https://github.com/epiverse-trace/packagetemplate/blob/59bbe3cafb1adf479b6e8d295e73c73ddca1d5d2/DESCRIPTION#L18-L20) is still in line with the current scope
- [x] Make sure links to GitHub repository and issue tracker are listed: `usethis::use_github_links()`
- [x] Re-order and standardize `DESCRIPTION` with `desc::desc_normalize()`
- [x] Submit a PR adding yourself as author to packagetemplate

## Final `R CMD check`

- [x] Run `devtools::check()` locally to catch `NOTE`s and `WARNING`s that can still easily slip through continuous integration
- [ ] devtools::check(remote = TRUE, manual = TRUE)
- [ ] devtools::check_win_devel(): cannot complete due to `curl` issues

## GitHub

- [ ] Check if issues are still relevant. If not, please close them, ideally with a link to the commit fixing them or a comment explaining why they no longer apply.
- [ ] Check if [discussions](https://github.com/orgs/epiverse-trace/discussions) you started are still ongoing. If not, please close the thread.