Drop the no-new-extensions rule and the stale submodule premise

.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

@@ -24,12 +24,10 @@ 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/workflows/claude-code-review.yml

@@ -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
@@ -72,15 +71,13 @@ 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/copilot-setup-steps.yml

@@ -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') }}

CLAUDE.md

@@ -4,7 +4,7 @@ Project guidance for Claude Code (CLI, IDE, and the GitHub Action). The same con
 
 ## Project context
 
-`mds` holds the mathematics that the Morrison-Lab data science courses assume: notation, algebra, calculus, linear algebra and vector calculus, as [Quarto](https://quarto.org/) fragments. It renders on its own as a website, and course sites include it as a git submodule, so a fragment's path and its `#id` anchors are an interface: renaming either breaks every host site. The scaffolding came from the UCD-SERG `qwt` template.
+`mds` holds the mathematics that the Morrison-Lab data science courses assume: notation, algebra, calculus, linear algebra and vector calculus, as [Quarto](https://quarto.org/) fragments. It renders on its own as a website, and course sites such as `mlds` link to its pages by URL, so a page's path and its `#id` anchors are an interface: renaming either breaks those links. The scaffolding came from the UCD-SERG `qwt` template.
 
 Authoritative style guide: [UCD-SERG Lab Manual](https://ucd-serg.github.io/lab-manual/) (source: <https://github.com/UCD-SERG/lab-manual>).
 
@@ -80,6 +80,5 @@ rme will drop those appendices and point readers here
 
 ## Things to avoid
 
-- Adding new top-level dependencies (R packages, Quarto extensions) without a clear reason; this is a template, so every dependency lands in every downstream book.
 - Reformatting unrelated files.
 - Inventing URLs or citations --- only use sources actually present in `references.bib` or explicitly provided.