[d-morrison]

Requested by Ezra · project thread

Part of #568 (closes it). Batch 3 of 3. Same change as batch 1 on the last 8 pages: every body heading moves up one level so sections number 1, 2, 3 instead of 0.1, 0.2. Heading text is unchanged. Merge with batches 1 and 2.

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Review of PR #571 (heading promotion: ## to #)

I read the diff and the heading structure around it. I did not render the site.

The PR changes 8 pages. On each, the trailing ## Further reading, ## References and ## The pages heading becomes #. It has no description, so I can't tell the intent.

Findings

1. Heading hierarchy is now inconsistent. (Needs a fix, or an explanation of why this is intended.)

   • The included fragments mds/_sets.qmd, mds/_relations.qmd and mds/_notation.qmd use ## for their sections. Examples are mds/_sets.qmd:126 and mds/_relations.qmd:11.
   • Because those sections have no # parent, the page now mixes ## sections from the include with # sections written in the page file.
   • Affected lines: sets.qmd:15, sets.qmd:34, notation.qmd:39, notation.qmd:55 and relations.qmd:15.
   • With number-sections: true (_quarto-website.yml:322), this can leave the included sections numbered like 0.1, with "Further reading" as a separate top-level 1. It also changes the table of contents nesting.
   • linear-algebra.qmd:60 and linear-algebra.qmd:89 still use ## for the same headings.
   • Pages like sets.qmd therefore now differ from linear-algebra.qmd. Please confirm this is intended and apply it to all pages, or revert.

2. Anchors look safe, but a numbered heading may have moved.

   • The #sec-... ids (#sec-further-reading, #sec-additional-resources, #sec-split-pages) are unchanged. External mlds links by URL and anchor should still work.
   • Any @sec-... reference that renders as "Section N.M" will change its number.

3. Possible numbering and styling change on sets-functions.qmd:36. This is a redirect stub whose single section "The pages" now becomes a top-level #. This is probably harmless.

4. No description. The PR has no title or description explaining why. The repo's PR expectations ask for the why.

I found no other problems.

Verdict

Needs more work. The ## to # promotion is applied to only some pages and conflicts with the ## headings in the included fragments. Please explain the intent or make the hierarchy consistent.

Structured Review Data (JSON)

{
  "schema_version": "1.1",
  "reviewer": "claude",
  "commit_sha": "7d8f83750e7f90d72cab2a51e635eb567a55cbed",
  "verdict": "NOT_CLEAN",
  "findings": [
    {"file": "sets.qmd", "line": 15, "category": "style", "message": "Further reading/References promoted to # while included fragments (mds/_sets.qmd etc.) use ##, and linear-algebra.qmd still uses ##; hierarchy and section numbering become inconsistent across pages."},
    {"file": "relations.qmd", "line": 15, "category": "style", "message": "References promoted to # but the included _relations.qmd sections are ##; confirm intended numbering and TOC nesting."}
  ],
  "detailed_assessment": "Heading promotion in sets.qmd, notation.qmd and relations.qmd mixes # headings with ## headings from included fragments, risking odd section numbering and TOC nesting, while linear-algebra.qmd keeps ##.",
  "holistic_assessment": "The PR has no description of intent, applies the change to only some pages, and may change rendered section numbers referenced by cross-references, though ids and URLs are preserved."
}

@claude address review comments in [this review](https://github.com/Morrison-Lab/mds/pull/571)

Reviewed commit: 7d8f837

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_{2026-11-02 21:47 UTC}