[dem-extra1]

Requested by Ezra · project thread

Important

Stacked on #806 (base claude/project-thread-j628gi). Merge #806 first, with a merge commit, then retarget this to main.

Closes #812.

Why

Ezra asked why the #806 preview shows 1389 definitions and results for mds alone, then only 886 for the tree that joins mds with mcs. Two causes, both in #812:

• The joined tree's data-json names mds's graph by its published URL, so a preview joins mcs with main's mds graph (723 mds + 162 mcs + 1 sds = 886), while the site tree shows the preview's own graph.
• Show the mcs prerequisites in a joined tree on the Dependency Tree page #806's branch predates Build the five umbrella pages as html only #748, so its umbrella pages still repeat each section in an unless-format="html" block, and the graph builder counts those divs twice (1389 instead of 724). That one goes away when Show the mcs prerequisites in a joined tree on the Dependency Tree page #806 is brought up to date with main; this PR doesn't touch it.

What changed

• dependency-tree.qmd: the joined tree names this site's graph as the relative dependency-graph.json, so a preview joins its own graph and the published site still gets the published one.
• dependency-graph.js: a joined tree says how many boxes come from each site, e.g. "887 definitions and results (162 from mcs, 724 from mds, 1 from sds), 1378 dependencies, 12 levels." The site tree's line is unchanged.
• lychee.toml: Show the mcs prerequisites in a joined tree on the Dependency Tree page #806's exact-match exclusion for the data-json string, updated to the new string.

Verification

Ran this branch's dependency-graph.js on the #806 preview page under jsdom (no browser), with the relative URL resolved against a preview path:

mds graph fed in	Site tree	Joined tree
built from current main	724, 875 deps, 10 levels	887 (162 mcs, 724 mds, 1 sds), 1378 deps, 12 levels
#806's preview graph	1389, 2440 deps, 13 levels	1552 (162 mcs, 1389 mds, 1 sds), 3135 deps, 15 levels

In both cases the joined tree's mds count now matches the site tree. The same counts come out of a Python re-implementation of the script's layering over the JSON files.

Not rendered with Quarto: the .qmd change is one attribute value. typos flags thm on line 23 of dependency-graph.js, which this PR doesn't touch.

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Generated by Claude Code

[github-actions]

Claude finished review — View run

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This confirming review finds no new issues. The diff against the base is the same three files as in the prior review of 2026-11-13, commit d9f9573, which gave Ready for merge. I re-read it, but did not run it or render the page.

The head moved to c26b9ac only through two merges, a86d2a4 and c26b9ac. Both match git's automatic merge of their parents. The other commits in the range are already on main, so they are not part of this PR's scope.

• dependency-tree.qmd:33: the data-json attribute now ends with the relative URL dependency-graph.json. It resolves against the page, so a PR preview joins its own graph instead of the published one.
• dependency-graph.js:215-221: the per-site counts run only when g.site is empty, which is the joined-tree call. The single-site tree line is unchanged. The sorted output is deterministic.
• lychee.toml:23: the exclusion regex matches the new data-json string exactly and keeps the old escaping.
• Prose, math and citation rules: the diff adds no notes prose, math, citations or R code, so those checks do not apply.

Verdict

Ready for merge

Structured Review Data (JSON)

{
  "schema_version": "1.1",
  "reviewer": "claude",
  "commit_sha": "c26b9ac05581feafd7dc361aea62f5e059232575",
  "verdict": "CLEAN",
  "findings": [],
  "detailed_assessment": "Re-read dependency-graph.js per-site counts, the relative data-json URL in dependency-tree.qmd, and the lychee.toml exclusion regex; all remain consistent and no failure mode was found.",
  "holistic_assessment": "The diff is unchanged since the prior clean round, the only new commits are clean merges of main and the base PR, and scope stays narrowly on issue 812 with no regression concern."
}

Reviewed commit: c26b9ac

[github-actions]

💰 Cost: $0.2199 (review) — run

[dem-extra1]

Non-Claude reads of this PR's own diff (against #806) at head c26b9ac, through the OpenCode Go endpoint's free ids (paid models at their weekly limit): beam-free CLEAN (reasoned: relative URL, per-site counts and lychee pattern consistent), iceman-contributor-free CLEAN. Head c26b9ac only merges #806's updated branch into this one; the diff above is unchanged.

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Posted by Claude Code (AI agent) --- not written by a human.

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Generated by Claude Code

[github-actions]

PR Preview Action v1.8.2
🚀 Preview available at: https://Morrison-Lab.github.io/mds/pr-preview/pr-813/

_{Built to branch gh-pages at 2026-11-13 06:11 UTC.}

[dem-extra1]

Annotation dispositions for head c26b9ac

All 51 annotations on this head's 47 check runs are notices; none is a warning or failure.

• 47 × "The ubuntu-latest label will migrate to Ubuntu 26": runner-image notice, not about this PR.
• 1 × "SUBMODULES_TOKEN is empty; cloning submodules anonymously": the only submodule (latex-macros) is public, and checkout succeeded.
• 1 × "PR edits workflow files; restored .github/workflows/ from the default branch": raised while this PR's base was Show the mcs prerequisites in a joined tree on the Dependency Tree page #806's branch, which was behind main. Now that Show the mcs prerequisites in a joined tree on the Dependency Tree page #806 is merged and the base is main, the PR changes only dependency-graph.js, dependency-tree.qmd and lychee.toml.
• 2 × "Skipping element-level diff highlighting: ... exceed the 500-element cap": the preview's change highlighter skipped two large pages; it affects only the preview's highlighting, not the build.

#806 is merged (merge commit af570c1), and this PR is retargeted to main.

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Posted by Claude Code (AI agent) --- not written by a human.

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Generated by Claude Code