Update Opakapaka case study and add back to github.io page

[iantaylor-NOAA]

What is the feature?

I updated the opakapaka case study to use r4ss::ss3_data_to_fims() which eliminates the need for all the custom code processing the weight-at-age and age-to-length-conversion inputs. The match with the SS3 isn't perfect, but it's pretty good and I think worth having the stock visible on the rendered github.io page.

How have you implemented the solution?

• Modify input processessing using new r4ss function (and point to the main branch of r4ss)
• Copy some calculations and the index plots from pacific-hake.qmd
• Add Opakapaka back to the rendered github.io page
• Change the title to "'Ōpakapaka" with the Hawaiian diacritical marks (the ʻokina and the kahakō) as shown on this NOAA page: https://www.fisheries.noaa.gov/species/crimson-jobfish-opakapaka

Does the PR impact any other area of the project, maybe another repo?

• No

[Copilot]

Pull request overview

Updates the PIFSC ‘Ōpakapaka case study to use the newer r4ss::ss3_data_to_fims() pathway (reducing custom SS3-to-FIMS data wrangling), and re-enables the case study in the rendered GitHub Pages site.

Changes:

• Refactors the ‘Ōpakapaka case study data-prep to use r4ss::ss3_data_to_fims() and updates plots/parameter setup accordingly.
• Adds the case study back into the Quarto render list + sidebar navigation (with Hawaiian diacritics in the title).
• Switches CI/devcontainer dependency install from an r4ss feature branch to github::r4ss/r4ss.

Reviewed changes

Copilot reviewed 5 out of 6 changed files in this pull request and generated 7 comments.

Show a summary per file

File	Description
content/PIFSC-opakapaka.qmd	Reworks SS3→FIMS data conversion and updates model setup/plots; re-titles the case study.
_quarto.yml	Adds the ‘Ōpakapaka case study back to rendering and sidebar nav.
.github/workflows/render.yml	Updates CI dependency install to pull r4ss from default branch.
.github/workflows/render-and-publish.yml	Updates publish workflow dependency install to pull r4ss from default branch.
.devcontainer/devcontainer.json	Updates devcontainer package list to pull r4ss from default branch.

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[iantaylor-NOAA]

@MOshima-PIFSC, if you're back and have any time to spare, you could look at these changes. Feel free to make additional changes, or raise any issues you find.