Set up cds as a fragment library

.Rbuildignore

@@ -12,6 +12,7 @@ _freeze/
 ^\.github$
 ^README\.Rmd$
 ^data-raw$
+^cds$
 ^\.quarto$
 ^AGENTS\.md$
 ^CLAUDE\.md$

.claude/commands/lint.md

@@ -1,10 +1,22 @@
 ---
 description: Lint all R source files and report issues
 allowed-tools:
+  - Bash(rm -f cds)
   - Bash(Rscript -e 'lintr::lint*')
 ---
 
-Run `Rscript -e 'lintr::lint_dir()'` to check all R source files against `.lintr.R`.
+First run `rm -f cds` to remove the repo's self-referential `cds -> .` symlink
+(see CLAUDE.md) from the working tree. `lintr::lint_dir()`'s own directory
+walk follows symlinks and has no config-level way to skip it (any
+`.lintr.R` exclusion naming `cds` collapses onto the real files it aliases
+and silently excludes them too --- see `.lintr.R`'s comment), so with the
+symlink present every real lint is duplicated dozens of times over. Removing
+it first is safe: it only deletes the symlink, never the directory it points
+into.
+
+Then run `Rscript -e 'lintr::lint_dir()'` to check all R source files against `.lintr.R`.
+Afterwards, whether or not lint succeeds, restore the symlink with
+`git checkout -- cds`, so the deletion is never committed.
 
 Report all lint issues grouped by file, including:
 

.claude/commands/new-chapter.md

@@ -1,33 +1,32 @@
 ---
-description: Scaffold a new chapter in the Quarto website
+description: Scaffold a new topic page in the Quarto website
 allowed-tools:
   - Read
   - Write
   - Edit
   - Bash(quarto render:*)
 ---
 
-Create a new chapter from `$ARGUMENTS` (e.g. `/new-chapter intro Introduction`).
+Create a new topic page from `$ARGUMENTS` (e.g. `/new-chapter intro Introduction`).
 
 First, parse `$ARGUMENTS`: the first whitespace-delimited token is the **slug**
 (used for the filename, no `.qmd`); everything after the first space is the
 **title** (default the title to the slug if none is given).
 
 Steps:
 
-1. Create `chapters/<slug>.qmd` with YAML frontmatter holding just `title:` (set
+1. Create `<slug>.qmd` at the repo root with YAML frontmatter holding just `title:` (set
    to the title). Do NOT set `date:` --- `_quarto-website.yml` sets
    `date: last-modified` globally, and a per-page `date:` would override it and
    freeze the date. Do NOT add a top-level `#` heading in the body --- Quarto
    renders the frontmatter `title:` as the page heading, so a `#` heading would
    duplicate it.
-2. Add an entry for the new chapter to the `website.navbar.left` "Chapters" menu
-   in `_quarto-website.yml` (read the file first to find the menu; there is no
-   `chapters:` key in `_quarto.yml`). Use `text:` for the menu label and
-   `href: chapters/<slug>.qmd`.
-   Also add `chapters/<slug>.qmd` to the "Chapters" section of `website.sidebar`
-   in the same position: the sidebar order sets the previous/next page links.
-3. Confirm it renders: `quarto render chapters/<slug>.qmd`.
+2. Add `<slug>.qmd` to `website.sidebar.contents` in `_quarto-website.yml`,
+   in reading order: the sidebar order sets the previous/next page links.
+   Add the same page, in the same position, to the matching menu under
+   `website.navbar.left` (create the `left:` list and menu if this is the
+   first page): the navbar menus mirror the sidebar one-for-one.
+3. Confirm it renders: `quarto render <slug>.qmd`.
 
 Style rules (from CLAUDE.md):
 

.github/copilot-instructions.md

@@ -30,12 +30,12 @@ When describing lists of three or more items, use a bullet list instead of a com
 
 **Examples:**
 
-❌ **Don't** use comma-separated lists for three or more items:
+**Don't** use comma-separated lists for three or more items:
 ```
 The template includes GitHub Actions workflows for publishing, link checking, and spell checking.
 ```
 
-✅ **Do** use bullet lists instead:
+**Do** use bullet lists instead:
 ```
 The template includes GitHub Actions workflows for:
 

.github/dependabot.yml

@@ -1,9 +1,8 @@
 # Keep git submodules and pinned GitHub Actions up to date automatically.
 #
-# This template embeds the shared `macros` repo as the `latex-macros` git submodule. Dependabot's
+# This repo embeds the shared `macros` repo as the `latex-macros` git submodule. Dependabot's
 # `gitsubmodule` updater opens a PR whenever a submodule's default branch
-# (currently `main`) advances, so neither this template nor the books generated
-# from it have to bump the pointer by hand. See the ADR at Morrison-Lab/macros
+# (currently `main`) advances, so the pointer never has to be bumped by hand. See the ADR at Morrison-Lab/macros
 # (docs/adr/0001-macros-submodule-versioning.md) for why we track `main` rather
 # than a pinned release tag.
 version: 2

.github/instructions/r-and-config.instructions.md

@@ -16,10 +16,8 @@ description: "Use when editing R source, Quarto configuration, or GitHub workflo
 - Run `Rscript -e 'spelling::spell_check_package()'` before finishing changes to
   `.R` or config files. Fix only errors you introduced, and add legitimate
   technical terms to `inst/WORDLIST` rather than disabling the check.
-- This is a template: every dependency added here lands in every downstream
-  book, so do not add a new R package or Quarto extension without a clear
-  reason. Align workflow and render changes with the existing CI patterns
-  instead of inventing parallel setup.
+- Align workflow and render changes with the existing CI patterns instead of
+  inventing parallel setup.
 - Do not edit generated files (`README.md` is built from `README.Rmd`; `_site/`,
   `_freeze/`, and `.quarto/` are build outputs).
 

.github/prompts/quarto-review.prompt.md

@@ -25,12 +25,10 @@ Review checklist:
    chunk and referenced with inline R.
 5. Citations and attribution are present where adapted content or factual
    claims appear, and only sources in `references.bib` are used.
-6. No new R package or Quarto extension is added without a clear reason (this is
-   a template --- every dependency lands in every downstream book).
-7. No generated files are edited (`README.md` from `README.Rmd`; `_site/`,
+6. No generated files are edited (`README.md` from `README.Rmd`; `_site/`,
    `_freeze/`, `.quarto/`), and spell/link-check failures are fixed at the
    source (wordlist or content), not suppressed.
-8. The author ran the required local validation:
+7. The author ran the required local validation:
    - render of the touched page
    - `lintr`
    - `spelling::spell_check_package()`

.github/rulesets/README.md

@@ -26,7 +26,7 @@ Applies to the default branch:
 - **No force-pushes, no branch deletion.**
 - **Copilot code review** runs on every push and on draft PRs.
 - **No mandatory approval by default** --- PRs require no approvals to merge
-  (`required_approving_review_count: 0`); raise this under Settings → Rules →
+  (`required_approving_review_count: 0`); raise this under Settings -> Rules ->
   Rulesets if you want a review gate.
 - **Bypass** in `pull_request` mode for the Maintain role (role id 2) ---
   Maintainers can merge pull requests even when the ruleset's PR requirements
@@ -35,7 +35,7 @@ Applies to the default branch:
 ## Editing the ruleset
 
 Edit `main.json` here, then run `apply-rulesets.sh` to push the change to
-the live repo. Or edit in the GitHub UI (Settings → Rules → Rulesets) and
+the live repo. Or edit in the GitHub UI (Settings -> Rules -> Rulesets) and
 re-export with:
 
 ```sh

.github/workflows/check-bibliography-dois.yml

@@ -20,4 +20,4 @@ jobs:
   check-dois:
     permissions:
       contents: read
-    uses: Morrison-Lab/gha/.github/workflows/check-bibliography-dois.yml@v2
+    uses: Morrison-Lab/gha/.github/workflows/check-bibliography-dois.yml@v3

.github/workflows/check-links.yml

@@ -4,7 +4,7 @@ name: Check Links
 # The reusable workflow reproduces the previous standalone behavior: lychee
 # link check over .qmd/.md/.html, a PR skip-label ("links checked by hand"),
 # and auto-filing an issue when links break on main. We pass our repo-local
-# lychee.toml so the qwt-specific excludes (e.g. quarto.org) still apply.
+# lychee.toml so the cds-specific excludes (e.g. quarto.org) still apply.
 # See https://github.com/Morrison-Lab/gha for inputs and versioning.
 
 on:
@@ -26,6 +26,6 @@ jobs:
       contents: read
       issues: write
       pull-requests: read
-    uses: Morrison-Lab/gha/.github/workflows/check-links.yml@v2
+    uses: Morrison-Lab/gha/.github/workflows/check-links.yml@v3
     with:
       lychee-config: lychee.toml

.github/workflows/claude-code-review.yml

@@ -5,7 +5,7 @@
 # line, and already skips drafts, Dependabot bumps, fork PRs, and PRs that
 # edit this workflow file itself (the action can't review its own diff --
 # see gha's own comments on the App-token validation 401). This caller only
-# supplies qwt's Quarto/R-specific review guidance on top.
+# supplies cds's Quarto/R-specific review guidance on top.
 # See https://github.com/Morrison-Lab/gha for inputs and versioning.
 #
 # Secrets are passed explicitly rather than via `secrets: inherit`: GitHub
@@ -41,15 +41,15 @@ jobs:
       contents: read
       pull-requests: write  # post review + inline comments
       issues: write
-      id-token: write        # required by claude-code-action for the App-token exchange
-      actions: read          # lets the reviewer read CI status
-    uses: Morrison-Lab/gha/.github/workflows/claude-code-review.yml@v2
+      actions: read          # lets the reviewer read CI status (github_ci MCP server)
+      checks: read           # required by v3 reusable workflow (gha#833)
+    uses: Morrison-Lab/gha/.github/workflows/claude-code-review.yml@v3
     secrets:
       CLAUDE_CODE_OAUTH_TOKEN: ${{ secrets.CLAUDE_CODE_OAUTH_TOKEN }}   # Max-plan OAuth; empty when using API key
       ANTHROPIC_API_KEY: ${{ secrets.ANTHROPIC_API_KEY }}               # direct API key; empty when using OAuth
       SUBMODULES_TOKEN: ${{ secrets.SUBMODULES_TOKEN }}   # optional; latex-macros/ is public, so unset is fine
     with:
-      pr-number: ${{ inputs.pr_number }}
+      pr-number: ${{ github.event.pull_request.number || inputs.pr_number }}
       checkout-submodules: true  # latex-macros/ so the reviewer can read it, not report it "not initialized"
       # `claude` is included because a remote Claude session pushing a
       # commit directly to a PR fires `synchronize` with `claude` as the
@@ -58,9 +58,8 @@ jobs:
       # "non-human actor".
       allowed-bots: 'github-actions[bot],claude'
       prompt-addendum: |
-        In addition to the standard checks above, this is the qwt Quarto
-        website template -- small, prose-heavy, and re-used as a template
-        for downstream books -- so also prioritize:
+        In addition to the standard checks above, this is a small,
+        prose-heavy Quarto website, so also prioritize:
 
         1. **Quarto / prose correctness**
            - `.qmd` syntax: chunk options use `#|` directives, fenced
@@ -73,15 +72,13 @@ jobs:
 
         2. **R code**
            - Conforms to `.lintr.R` settings (snake_case, line length, etc.).
-           - No new package dependencies without justification -- every
-             dependency added here lands in every downstream book.
 
         3. **Build hygiene**
            - No accidental commits of `_site/`, `_freeze/`, or `.quarto/`.
            - `README.md` is generated; edits should go to `README.Rmd`.
            - Bibliography entries in `references.bib` are well-formed BibTeX.
 
-        4. **CI / template impact**
+        4. **CI impact**
            - Workflow changes don't break the `copilot-setup-steps.yml`
              contract or the publish/preview pipelines.
            - Spell-check / link-check failures are fixed at the source

.github/workflows/claude.yml

@@ -8,7 +8,7 @@
 # posting Claude's prose reply when no code was committed, dispatching
 # claude-code-review.yml on an explicit "@claude review" (including one
 # absorbed late by the polling loop), and the late-comment dedup / rescue
-# machinery (`<!-- claude-absorbed: ... -->` marker + 🚀 reaction) that was
+# machinery (`<!-- claude-absorbed: ... -->` marker + rocket reaction) that was
 # originally ported FROM this repo's own #73/#90/#95 into gha's claude.yml.
 # See https://github.com/Morrison-Lab/gha for inputs and versioning.
 #
@@ -53,12 +53,12 @@ jobs:
       issues: write         # so Claude can comment on issues
       id-token: write
       actions: write        # dispatch claude-code-review.yml via `gh workflow run`
-    uses: Morrison-Lab/gha/.github/workflows/claude.yml@v2
+    uses: Morrison-Lab/gha/.github/workflows/claude.yml@v3
     secrets:
       CLAUDE_CODE_OAUTH_TOKEN: ${{ secrets.CLAUDE_CODE_OAUTH_TOKEN }}   # Max-plan OAuth; empty when using API key
       ANTHROPIC_API_KEY: ${{ secrets.ANTHROPIC_API_KEY }}               # direct API key; empty when using OAuth
       SUBMODULES_TOKEN: ${{ secrets.SUBMODULES_TOKEN }}   # optional; latex-macros/ is public, so unset is fine
       WORKFLOW_TOKEN: ${{ secrets.WORKFLOW_TOKEN }}       # optional; for editing .github/workflows
     with:
-      install-quarto: true      # qwt is a Quarto site; Claude may need to render .qmd files
+      install-quarto: true      # cds is a Quarto site; Claude may need to render .qmd files
       checkout-submodules: true # latex-macros/ (public; no SUBMODULES_TOKEN needed)

.github/workflows/copilot-setup-steps.yml

@@ -1,4 +1,4 @@
-# GitHub Copilot Setup Steps for qwt
+# GitHub Copilot Setup Steps for cds
 #
 # This workflow configures the GitHub Copilot coding agent's environment
 # by preinstalling R, Quarto, TinyTeX, and system dependencies.
@@ -54,7 +54,7 @@ jobs:
         id: check_label
         # Pass the expression result through env (GitHub-recommended) rather
         # than interpolating it directly into the shell, to avoid the
-        # expression-injection anti-pattern in code that downstream books copy.
+        # expression-injection anti-pattern.
         env:
           EVENT_NAME: ${{ github.event_name }}
           LABELS_CONTAIN_SKIP: ${{ contains(github.event.pull_request.labels.*.name, 'skip-cp-setup') }}

.github/workflows/lint-changed-files.yaml

@@ -25,6 +25,18 @@ jobs:
     steps:
       - uses: actions/checkout@v7
 
+      # `cds` is a self-referential symlink (`cds -> .`, see CLAUDE.md). Left
+      # in place, `all_files` below would also list every real file a second
+      # time under `cds/...`, and lintr's exclusions field always resolves
+      # through normalize_path() (see .lintr.R), which follows symlinks: a
+      # `cds/<changed-file>` entry in `all_files` normalizes onto the exact
+      # same path as the real changed file, so `setdiff(all_files,
+      # changed_files)` -- which only strips the real path, never its
+      # cds-prefixed alias -- ends up excluding the real changed file too.
+      # Removing the symlink up front avoids both problems.
+      - name: Remove self-referential cds symlink before linting
+        run: rm -f cds
+
       - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true

.github/workflows/lint-project.yaml

@@ -17,6 +17,17 @@ jobs:
     steps:
       - uses: actions/checkout@v7
 
+      # `cds` is a self-referential symlink (`cds -> .`, see CLAUDE.md) that
+      # lets include paths written as `cds/...` resolve when this repo
+      # renders standalone. lintr's own directory walk follows symlinks and
+      # has no config-level way to exclude it without also excluding the
+      # real files it aliases (normalize_path() collapses the two onto the
+      # same path -- see .lintr.R). Remove it before linting so lintr never
+      # walks into it; nothing under it is content distinct from what's
+      # already linted at the repo root, and this job never renders the site.
+      - name: Remove self-referential cds symlink before linting
+        run: rm -f cds
+
       - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true

.github/workflows/preview.yml

@@ -52,8 +52,8 @@ jobs:
       changed-chapters-banner: true
       highlight-changes: ${{ !contains(github.event.pull_request.labels.*.name, 'no-preview-highlights') }}
       docx-tracked-changes: true
-      # The home page plus chapters/, and the slide decks that sit beside them
-      # (gha's default `chapters/*.html` and `chapters/*.docx` would miss index).
+      # Pages render at the site root, beside their slide decks
+      # (gha's default `chapters/*.html` and `chapters/*.docx` would miss them).
       changed-chapters-glob: '**/*.html'
       docx-tracked-changes-glob: '**/*.docx'
 

.github/workflows/summary.yml

@@ -20,4 +20,4 @@ jobs:
       issues: write
       models: read
       contents: read
-    uses: Morrison-Lab/gha/.github/workflows/summary.yml@v2
+    uses: Morrison-Lab/gha/.github/workflows/summary.yml@v3

.gitignore

@@ -9,7 +9,6 @@
 # Source HTML partials we intentionally track (not build output).
 !qwt-reveal-toggle.html
 !theme-picker.html
-!page-navigation.html
 *_files/
 site_libs/
 
@@ -78,3 +77,6 @@ renv/staging/
 # Lychee link checker
 .lycheecache/
 lychee-output/
+
+# pak lockfile
+.github/pkg.lock

.lintr.R

@@ -27,4 +27,17 @@ exclusions <- list(
   `data-raw` = list(
     pipe_consistency_linter = Inf
   )
+
+  # NOTE: `cds` (the self-referential `cds -> .` symlink -- see CLAUDE.md) is
+  # NOT excluded here on purpose. lintr::lint_dir()/lint_package() resolve
+  # every exclusion path through normalize_path() (lintr:::normalize_exclusions()),
+  # which follows symlinks. Because `cds` points at the repo root, ANY
+  # exclusion naming it -- the directory itself, or any file path under it --
+  # normalizes to the exact same absolute path as the real file it aliases,
+  # so it silently excludes the real file too, not just the symlinked
+  # duplicate. There is no exclusions-list syntax that can single out the
+  # duplicate without also matching the original. The actual fix lives in
+  # the CI workflows (lint-project.yaml, lint-changed-files.yaml), which
+  # remove the `cds` symlink from the checkout before invoking lintr at all,
+  # so lintr's own directory walk never sees it and no exclusion is needed.
 )

AGENTS.md

@@ -9,4 +9,9 @@ the ai-config plugin), read
 before starting work, and follow it alongside this file.
 This file's own instructions add to those rules, and win only where they are
 more specific.
+
+Also follow the [UCD-SERG Lab Manual](https://ucd-serg.github.io/lab-manual/)
+(source: <https://github.com/UCD-SERG/lab-manual>) and, for prose,
+[*Principles of Scientific Writing*](https://morrison-lab.github.io/psw/)
+(source: <https://github.com/Morrison-Lab/psw>).
 <!-- ai-config:end -->