Document dependency setup paths with and without renv

[Copilot]

This issue asked for README guidance on package installation now that setup code was removed from setup.qmd. This update adds explicit dependency setup instructions for both renv and non-renv workflows.

• Dependency setup guidance

  • Added a new R package dependencies section in README.md.
  • Documents renv workflow when a lockfile is present.
  • Documents non-renv workflow by pointing to the maintained dependency sources:
    • .github/workflows/render.yml
    • .github/workflows/render-and-publish.yml
    • .devcontainer/devcontainer.json

• Scope

  • README-only update; no codepath or workflow logic changes.

install.packages("renv")
renv::restore()

[iantaylor-NOAA]

@copilot, the changes are better than nothing, but I was imagining a more user-friendly approach that doesn't require manually copying and pasting the package names (and their github repos in some cases) into pak::pak(), like the loop previously used in setup.qmd:
https://github.com/NOAA-FIMS/case-studies/blob/4864870f4d9a962a7cb4ffe5737e95e282db38f1/content/setup.qmd

However, it would be nice to have a single list of package dependencies used throughout rather than trying to keep in sync the different yml files and the README. Any big-picture ideas along these lines would be helpful.

[Copilot]

@copilot, the changes are better than nothing, but I was imagining a more user-friendly approach that doesn't require manually copying and pasting the package names (and their github repos in some cas...

Addressed in commit 3bb6e65.

README now includes a non-renv install snippet that reads package dependencies directly from .github/workflows/render.yml and installs them via pak::pak(deps), so users don’t need to manually copy package names. I also added a concrete single-source direction: move to one canonical dependency file (e.g., config/r-packages.txt) that workflows, devcontainer setup, and local install docs can all consume.

[iantaylor-NOAA]

@copilot, this is helpful and the R script added to README worked well for me. Please make the one additional changes as suggested.

[iantaylor-NOAA]

Delete this line since it's been moved into a separate issue: #111

[Copilot]

@copilot, this is helpful and the R script added to README worked well for me. Please make the one additional changes as suggested.

Done in commit e01a627.

[MOshima-PIFSC]

I tested the non-renv steps and it works. I thought about switching the code to tidy-style to match with the rest of the FIMS code base but then realized the user may have to install some packages first to do that (e.g. purrr, stringr, etc) which would create more steps so I think using base functions is best.
The changes look good and I think its good to merge.