fix: add the 8 Reference pages missing from the website sidebar

[d-morrison]

Closes #273

The bug

website/_quarto.yml's "Reference" sidebar omitted several existing reference pages, so they were reachable only by direct URL or via website/workflows.qmd's catalog links.

Scope re-derived (8, not the issue's 4)

#273 (2026-07-18) listed 4 missing pages. Re-running its own verification against current main found 8 -- more capabilities were added since without sidebar entries:

for f in website/reference/*.qmd; do
  b=$(basename "$f")
  grep -q "reference/$b" website/_quarto.yml || echo "MISSING: $b"
done

Missing: lint-yaml, lint-markdown, check-new-line-breaks, lint-qmd, lint-changed-lines, check-equation-renders, request-dependabot-review, altdoc-multiversion-docs.

The fix

Each entry is inserted at its canonical position, so the sidebar order stays byte-identical to workflows.qmd's catalog order -- no existing entries reordered.

Verified:

• Every website/reference/*.qmd is now listed in the sidebar (the check above prints nothing).
• Every sidebar reference/*.qmd entry resolves to a real file.
• website/_quarto.yml parses as YAML.
• diff of the sidebar order against workflows.qmd's catalog order is empty (identical).

Adds a changelog.d/ fragment, matching the repo's precedent (document-update-snapshots.added.md) for website reference/sidebar doc changes.

[Copilot]

Copilot was unable to review this pull request because the user who requested the review has reached their quota limit.

[github-actions]

PR Preview Action v1.8.1
🚀 Preview available at: https://Morrison-Lab.github.io/gha/pr-preview/pr-429/

_{Built to branch gh-pages at 2026-08-06 09:50 UTC.}

[github-actions]

Claude finished review — View run

---

Code Review: #429

PR: "fix: add the 8 Reference pages missing from the website sidebar" (closes #273)

Summary: This PR adds 8 missing - reference/<name>.qmd entries to website/_quarto.yml's sidebar (lint-yaml, lint-markdown, check-new-line-breaks, lint-qmd, lint-changed-lines, check-equation-renders, request-dependabot-review, altdoc-multiversion-docs), each inserted at the position matching website/workflows.qmd's catalog order, plus a new changelog fragment (changelog.d/add-missing-sidebar-reference-entries.fixed.md) documenting the fix. No functional code, workflow, or composite-action files are touched.

Review process: Four independent agents (two for CLAUDE.md compliance, two for bugs/logic issues) checked out the PR's actual merged state and empirically verified every claim rather than trusting the PR description, per this repo's own "never just theorize" and "completeness claim ... needs the grep before it ships" guidance:

• Completeness claim verified true: website/reference/*.qmd contains exactly 33 files, and website/_quarto.yml's sidebar now contains exactly 33 matching reference/*.qmd entries — 1:1, no gaps, no dangling links, no duplicates.
• Ordering claim verified true: the sidebar order after this PR is identical, entry-for-entry, to website/workflows.qmd's catalog table order across all 33 capabilities, including all three insertion points.
• YAML validity confirmed: website/_quarto.yml parses cleanly; all 8 new entries sit at the correct 10-space indentation matching siblings.
• Changelog fragment: filename/category (.fixed.md) follows changelog.d/README.md's documented convention; the 8 names listed in the fragment exactly match the 8 names added to _quarto.yml in the same diff.
• Doc-sync scope check: grepped the whole repo for reference/ path enumeration — only _quarto.yml and workflows.qmd enumerate this set as a group, and workflows.qmd was already complete (it's the source this PR used for ordering), so no other file needed updating.

No CLAUDE.md violations and no bugs were found by any of the four review passes. No issues survived to the validation stage (step 5), since none were raised in step 4.

One non-blocking observation (not a compliance finding): issue #273 itself suggested adding this grep as a _selftest.yml step so a future reference page can't land without a sidebar entry again — this PR doesn't act on that suggestion, and the issue's own 4→8 drift between filing and merge is evidence it might be worth a follow-up. Not blocking.

Verdict

Ready for merge.

[github-actions]

💰 Cost: $4.6369 (review) — run

[d-morrison]

ARD summary

Verdict Ready for merge on the first round -- all completeness/ordering/YAML claims independently verified by the review, no threads, no blocking findings.

One non-blocking observation (the _selftest.yml sidebar-completeness guard #273 suggested): Deferred to #430. It's a valuable recurrence-preventer -- the 4->8 drift between #273's filing and this merge proves manual upkeep doesn't hold -- but it's a distinct workflow change (a new selftest step/script) that deserves its own focused PR rather than expanding this doc-completeness fix. #430 captures the grep and an optional order-sync assertion.